[{"type":"conference","abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","ddc":["600"],"status":"public","_id":"12548","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","file_size":1183339,"content_type":"application/pdf","creator":"fkarimip","relation":"main_file","file_id":"12549","checksum":"c253bee25e6dfe484f96662daa119cb6","success":1,"date_created":"2023-02-14T07:58:26Z","date_updated":"2023-02-14T07:58:26Z"}],"day":"08","has_accepted_license":"1","article_processing_charge":"No","publication":"2022 IEEE International Conference on Data Mining Workshops","citation":{"ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093."},"date_published":"2023-02-08T00:00:00Z","article_number":"00093","file_date_updated":"2023-02-14T07:58:26Z","publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"HeEd"}],"year":"2023","date_updated":"2023-08-01T13:15:48Z","date_created":"2023-02-14T07:56:21Z","author":[{"last_name":"Forghani","first_name":"Mohammad","full_name":"Forghani, Mohammad"},{"last_name":"Claramunt","first_name":"Christophe","full_name":"Claramunt, Christophe"},{"first_name":"Farid","last_name":"Karimipour","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","orcid":"0000-0001-6746-4174","full_name":"Karimipour, Farid"},{"last_name":"Heiler","first_name":"Georg","full_name":"Heiler, Georg"}],"month":"02","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000971492200145"]},"language":[{"iso":"eng"}],"conference":{"name":"ICDMW: Conference on Data Mining Workshops","start_date":"2022-11-28","location":"Orlando, FL, United States","end_date":"2022-12-01"},"doi":"10.1109/icdmw58026.2022.00093"},{"publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"month":"01","doi":"10.1137/20m1378223","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2003.11351"],"isi":["000955000000001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","ec_funded":1,"author":[{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"full_name":"Opršal, Jakub","last_name":"Opršal","first_name":"Jakub","orcid":"0000-0003-1245-3456","id":"ec596741-c539-11ec-b829-c79322a91242"},{"last_name":"Wrochna","first_name":"Marcin","full_name":"Wrochna, Marcin"},{"full_name":"Živný, Stanislav","last_name":"Živný","first_name":"Stanislav"}],"volume":52,"date_created":"2023-02-16T07:03:52Z","date_updated":"2023-08-01T13:11:30Z","year":"2023","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","department":[{"_id":"UlWa"}],"publisher":"Society for Industrial & Applied Mathematics","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["General Mathematics","General Computer Science"],"date_published":"2023-01-01T00:00:00Z","citation":{"ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223."},"publication":"SIAM Journal on Computing","page":"38-79","article_type":"original","issue":"1","abstract":[{"text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"12563","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 52","status":"public","title":"Topology and adjunction in promise constraint satisfaction"},{"month":"01","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01856","open_access":"1"}],"oa":1,"external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevE.107.014608","language":[{"iso":"eng"}],"article_number":"014608","year":"2023","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GradSch"}],"author":[{"full_name":"Rojas Vega, Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","first_name":"Mauricio Nicolas","last_name":"Rojas Vega"},{"last_name":"De Castro","first_name":"Pablo","full_name":"De Castro, Pablo"},{"last_name":"Soto","first_name":"Rodrigo","full_name":"Soto, Rodrigo"}],"date_created":"2023-02-12T23:00:59Z","date_updated":"2023-08-01T13:09:45Z","volume":107,"scopus_import":"1","day":"24","article_processing_charge":"No","publication":"Physical Review E","citation":{"short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608."},"article_type":"original","date_published":"2023-01-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12545","status":"public","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","intvolume":" 107","oa_version":"Preprint"},{"main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03013498/"}],"oa":1,"external_id":{"isi":["000898440000001"]},"isi":1,"quality_controlled":"1","doi":"10.1090/proc/15239","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"year":"2023","publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"TiBr"}],"author":[{"first_name":"Francesca","last_name":"Balestrieri","id":"3ACCD756-F248-11E8-B48F-1D18A9856A87","full_name":"Balestrieri, Francesca"}],"date_updated":"2023-08-01T13:03:32Z","date_created":"2023-01-29T23:00:58Z","volume":151,"publication":"Proceedings of the American Mathematical Society","citation":{"ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239","ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239.","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914.","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239."},"article_type":"original","page":"907-914","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12427","title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","status":"public","intvolume":" 151","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent."}],"issue":"3"},{"external_id":{"isi":["000994473300001"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.neuron.2023.01.006","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4199"]},"month":"02","year":"2023","publisher":"Elsevier","department":[{"_id":"SiHi"}],"publication_status":"published","author":[{"full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","first_name":"Ana","last_name":"Villalba Requena"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"volume":111,"date_updated":"2023-08-01T13:10:27Z","date_created":"2023-02-12T23:00:58Z","citation":{"chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006.","mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","apa":"Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006"},"publication":"Neuron","page":"291-293","article_type":"letter_note","date_published":"2023-02-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","_id":"12542","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 111","title":"Going back in time with TEMPO","status":"public","oa_version":"None","type":"journal_article","issue":"3","abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}]},{"article_number":"2128","file_date_updated":"2023-02-20T07:09:27Z","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","year":"2023","department":[{"_id":"PeJo"}],"publisher":"MDPI","publication_status":"published","author":[{"last_name":"Mrestani","first_name":"Achmed","full_name":"Mrestani, Achmed"},{"first_name":"Katharina","last_name":"Lichter","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","full_name":"Lichter, Katharina"},{"full_name":"Sirén, Anna Leena","first_name":"Anna Leena","last_name":"Sirén"},{"full_name":"Heckmann, Manfred","first_name":"Manfred","last_name":"Heckmann"},{"first_name":"Mila M.","last_name":"Paul","full_name":"Paul, Mila M."},{"last_name":"Pauli","first_name":"Martin","full_name":"Pauli, Martin"}],"volume":24,"date_updated":"2023-08-01T13:16:36Z","date_created":"2023-02-19T23:00:56Z","publication_identifier":{"eissn":["1422-0067"]},"month":"01","external_id":{"isi":["000930324700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.3390/ijms24032128","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","abstract":[{"text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12567","intvolume":" 24","ddc":["570"],"status":"public","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","file":[{"file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access","file_size":2823025,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12569","date_created":"2023-02-20T07:09:27Z","date_updated":"2023-02-20T07:09:27Z","checksum":"69a35dcd3e0249f902ab881b06ee2e58","success":1}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"21","citation":{"ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128."},"publication":"International Journal of Molecular Sciences","article_type":"original","date_published":"2023-01-21T00:00:00Z"},{"month":"02","publication_identifier":{"issn":["0304-3975"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2023.113733","quality_controlled":"1","isi":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000934262700001"]},"file_date_updated":"2023-02-20T07:30:20Z","ec_funded":1,"article_number":"113733","date_updated":"2023-08-01T13:17:20Z","date_created":"2023-02-19T23:00:55Z","volume":948,"author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Ellen, Faith","last_name":"Ellen","first_name":"Faith"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Elsevier","year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","day":"28","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-02-28T00:00:00Z","article_type":"original","publication":"Theoretical Computer Science","citation":{"chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733"},"abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","creator":"dernst","content_type":"application/pdf","file_size":602333,"file_id":"12570","relation":"main_file","success":1,"checksum":"b27c5290f2f1500c403494364ee39c9f","date_updated":"2023-02-20T07:30:20Z","date_created":"2023-02-20T07:30:20Z"}],"status":"public","title":"Wait-free approximate agreement on graphs","ddc":["000"],"intvolume":" 948","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12566"},{"scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"675-705","publication":"Annual Review of Fluid Mechanics","citation":{"short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705."},"date_published":"2023-01-19T00:00:00Z","type":"journal_article","abstract":[{"text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT.","lang":"eng"}],"issue":"1","status":"public","title":"Elasto-inertial turbulence","ddc":["530"],"intvolume":" 55","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12681","file":[{"relation":"main_file","file_id":"12690","date_created":"2023-02-27T09:23:02Z","date_updated":"2023-02-27T09:23:02Z","checksum":"2666aa3af2a25252d35eb8681d3edff7","success":1,"file_name":"2023_AnnReviewFluidMech_Dubief.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4036706,"creator":"dernst"}],"oa_version":"Published Version","month":"01","publication_identifier":{"issn":["0066-4189"],"eissn":["1545-4479"]},"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000915418100026"]},"language":[{"iso":"eng"}],"doi":"10.1146/annurev-fluid-032822-025933","file_date_updated":"2023-02-27T09:23:02Z","publication_status":"published","publisher":"Annual Reviews","department":[{"_id":"BjHo"}],"acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","year":"2023","date_updated":"2023-08-01T13:19:47Z","date_created":"2023-02-26T23:01:01Z","volume":55,"author":[{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"full_name":"Terrapon, Vincent E.","first_name":"Vincent E.","last_name":"Terrapon"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}]},{"publication_identifier":{"issn":["0066-4189"]},"month":"01","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000915418100023"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1146/annurev-fluid-120720-025957","file_date_updated":"2023-02-27T09:35:52Z","publisher":"Annual Reviews","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","year":"2023","volume":55,"date_created":"2023-02-26T23:01:01Z","date_updated":"2023-08-01T13:20:30Z","author":[{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"full_name":"Barkley, Dwight","first_name":"Dwight","last_name":"Barkley"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"19","page":"575-602","article_type":"original","citation":{"chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023.","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957"},"publication":"Annual Review of Fluid Mechanics","date_published":"2023-01-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed."}],"intvolume":" 55","title":"Transition to turbulence in pipe flow","ddc":["530"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12682","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_AnnReviewFluidMech_Avila.pdf","creator":"dernst","content_type":"application/pdf","file_size":4769537,"file_id":"12691","relation":"main_file","success":1,"checksum":"f99ef30f76cabc9e5e1946b380c16db4","date_updated":"2023-02-27T09:35:52Z","date_created":"2023-02-27T09:35:52Z"}]},{"month":"02","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000940388100001"],"arxiv":["2204.10059"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"doi":"10.1039/d2sm01562e","language":[{"iso":"eng"}],"file_date_updated":"2023-03-07T09:19:41Z","ec_funded":1,"year":"2023","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"Royal Society of Chemistry","author":[{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"last_name":"Janssen","first_name":"Liesbeth M.C.","full_name":"Janssen, Liesbeth M.C."},{"first_name":"Thomas","last_name":"Barois","full_name":"Barois, Thomas"},{"last_name":"Boffetta","first_name":"Guido","full_name":"Boffetta, Guido"},{"first_name":"Itai","last_name":"Cohen","full_name":"Cohen, Itai"},{"first_name":"Alessandro","last_name":"Corbetta","full_name":"Corbetta, Alessandro"},{"last_name":"Dauchot","first_name":"Olivier","full_name":"Dauchot, Olivier"},{"last_name":"Dijkstra","first_name":"Marjolein","full_name":"Dijkstra, Marjolein"},{"last_name":"Durham","first_name":"William M.","full_name":"Durham, William M."},{"last_name":"Dussutour","first_name":"Audrey","full_name":"Dussutour, Audrey"},{"full_name":"Garnier, Simon","last_name":"Garnier","first_name":"Simon"},{"full_name":"Gelderblom, Hanneke","first_name":"Hanneke","last_name":"Gelderblom"},{"full_name":"Golestanian, Ramin","last_name":"Golestanian","first_name":"Ramin"},{"first_name":"Lucio","last_name":"Isa","full_name":"Isa, Lucio"},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"full_name":"Löwen, Hartmut","first_name":"Hartmut","last_name":"Löwen"},{"full_name":"Metzler, Ralf","first_name":"Ralf","last_name":"Metzler"},{"full_name":"Polin, Marco","first_name":"Marco","last_name":"Polin"},{"full_name":"Royall, C. Patrick","last_name":"Royall","first_name":"C. Patrick"},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Sengupta, Anupam","first_name":"Anupam","last_name":"Sengupta"},{"first_name":"Cécile","last_name":"Sykes","full_name":"Sykes, Cécile"},{"first_name":"Vito","last_name":"Trianni","full_name":"Trianni, Vito"},{"full_name":"Tuval, Idan","last_name":"Tuval","first_name":"Idan"},{"full_name":"Vogel, Nicolas","last_name":"Vogel","first_name":"Nicolas"},{"full_name":"Yeomans, Julia M.","last_name":"Yeomans","first_name":"Julia M."},{"last_name":"Zuriguel","first_name":"Iker","full_name":"Zuriguel, Iker"},{"full_name":"Marin, Alvaro","last_name":"Marin","first_name":"Alvaro"},{"first_name":"Giorgio","last_name":"Volpe","full_name":"Volpe, Giorgio"}],"date_updated":"2023-08-01T13:28:39Z","date_created":"2023-03-05T23:01:06Z","volume":19,"scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"Soft Matter","citation":{"ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e."},"article_type":"original","page":"1695-1704","date_published":"2023-02-06T00:00:00Z","type":"journal_article","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12708","status":"public","title":"Steering self-organisation through confinement","ddc":["540"],"intvolume":" 19","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_SoftMatter_Araujo.pdf","content_type":"application/pdf","file_size":3581939,"creator":"cchlebak","relation":"main_file","file_id":"12711","checksum":"af95aa18b9b01e32fb8f13477c0e2687","success":1,"date_created":"2023-03-07T09:19:41Z","date_updated":"2023-03-07T09:19:41Z"}]},{"file":[{"access_level":"open_access","file_name":"2023_NatComm_Cheng.pdf","creator":"cchlebak","file_size":1946443,"content_type":"application/pdf","file_id":"12713","relation":"main_file","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","date_created":"2023-03-07T10:58:00Z","date_updated":"2023-03-07T10:58:00Z"}],"oa_version":"Published Version","_id":"12702","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 14","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","ddc":["540"],"status":"public","abstract":[{"lang":"eng","text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution."}],"type":"journal_article","date_published":"2023-02-27T00:00:00Z","citation":{"ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1."},"publication":"Nature Communications","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"27","scopus_import":"1","author":[{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"first_name":"Sebastien","last_name":"Hamel","full_name":"Hamel, Sebastien"},{"full_name":"Bethkenhagen, Mandy","first_name":"Mandy","last_name":"Bethkenhagen","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129"}],"volume":14,"date_updated":"2023-08-01T13:36:11Z","date_created":"2023-03-05T23:01:04Z","pmid":1,"acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","year":"2023","department":[{"_id":"BiCh"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2023-03-07T10:58:00Z","article_number":"1104","doi":"10.1038/s41467-023-36841-1","language":[{"iso":"eng"}],"external_id":{"isi":["000939678300002"],"pmid":["36843123"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"02"},{"type":"journal_article","abstract":[{"text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.","lang":"eng"}],"intvolume":" 15","title":"Refining epigenetic prediction of chronological and biological age","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12719","file":[{"file_id":"12722","relation":"main_file","success":1,"checksum":"833b837910c4db42fb5f0f34125f77a7","date_updated":"2023-03-14T10:29:47Z","date_created":"2023-03-14T10:29:47Z","access_level":"open_access","file_name":"2023_GenomeMed_Bernabeu.pdf","creator":"cchlebak","file_size":4275987,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"28","article_type":"original","citation":{"apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y","chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y."},"publication":"Genome Medicine","date_published":"2023-02-28T00:00:00Z","article_number":"12","file_date_updated":"2023-03-14T10:29:47Z","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","year":"2023","volume":15,"date_updated":"2023-08-01T13:38:12Z","date_created":"2023-03-12T23:01:02Z","author":[{"first_name":"Elena","last_name":"Bernabeu","full_name":"Bernabeu, Elena"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."},{"first_name":"Ake T.","last_name":"Lu","full_name":"Lu, Ake T."},{"last_name":"Murphy","first_name":"Lee","full_name":"Murphy, Lee"},{"full_name":"Wrobel, Nicola","last_name":"Wrobel","first_name":"Nicola"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"last_name":"Harris","first_name":"Sarah E.","full_name":"Harris, Sarah E."},{"full_name":"Liewald, David","first_name":"David","last_name":"Liewald"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"full_name":"Sudlow, Cathie","last_name":"Sudlow","first_name":"Cathie"},{"last_name":"Cox","first_name":"Simon R.","full_name":"Cox, Simon R."},{"last_name":"Evans","first_name":"Kathryn L.","full_name":"Evans, Kathryn L."},{"first_name":"Steve","last_name":"Horvath","full_name":"Horvath, Steve"},{"first_name":"Andrew M.","last_name":"Mcintosh","full_name":"Mcintosh, Andrew M."},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"first_name":"Catalina A.","last_name":"Vallejos","full_name":"Vallejos, Catalina A."},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."}],"publication_identifier":{"eissn":["1756-994X"]},"month":"02","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000940286600001"]},"language":[{"iso":"eng"}],"doi":"10.1186/s13073-023-01161-y"},{"volume":8,"date_created":"2023-03-05T23:01:04Z","date_updated":"2023-08-01T13:36:50Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"11366"}]},"author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"first_name":"Alexander","last_name":"Amini","full_name":"Amini, Alexander"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"department":[{"_id":"ToHe"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","year":"2023","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","file_date_updated":"2023-03-07T12:22:23Z","language":[{"iso":"eng"}],"doi":"10.1109/LRA.2023.3240930","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2204.07373"],"isi":["000936534100012"]},"publication_identifier":{"eissn":["2377-3766"]},"month":"03","file":[{"relation":"main_file","file_id":"12714","date_updated":"2023-03-07T12:22:23Z","date_created":"2023-03-07T12:22:23Z","checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1,"file_name":"2023_IEEERobAutLetters_Lechner.pdf","access_level":"open_access","file_size":944052,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","intvolume":" 8","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","status":"public","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12704","issue":"3","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-01T00:00:00Z","page":"1595-1602","article_type":"original","citation":{"mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930"},"publication":"IEEE Robotics and Automation Letters","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2023-03-08T00:00:00Z","page":"4625-4636","article_type":"original","citation":{"chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057.","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636.","ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","ieee":"Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057","ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057"},"publication":"Inorganic Chemistry","issue":"11","abstract":[{"lang":"eng","text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed."}],"type":"journal_article","oa_version":"None","intvolume":" 62","status":"public","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12737","publication_identifier":{"issn":["0020-1669"],"eissn":["1520-510X"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1021/acs.inorgchem.3c00057","quality_controlled":"1","isi":1,"external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"volume":62,"date_created":"2023-03-19T23:00:59Z","date_updated":"2023-08-01T13:42:59Z","author":[{"first_name":"Álvaro","last_name":"García-Romero","full_name":"García-Romero, Álvaro"},{"full_name":"Waters, Jessica E.","first_name":"Jessica E.","last_name":"Waters"},{"orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B"},{"full_name":"Bond, Andrew D.","last_name":"Bond","first_name":"Andrew D."},{"first_name":"Annie L.","last_name":"Colebatch","full_name":"Colebatch, Annie L."},{"first_name":"Raúl","last_name":"García-Rodríguez","full_name":"García-Rodríguez, Raúl"},{"full_name":"Wright, Dominic S.","first_name":"Dominic S.","last_name":"Wright"}],"publisher":"American Chemical Society","department":[{"_id":"StFr"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used."},{"date_published":"2023-03-10T00:00:00Z","citation":{"ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901."},"publication":"Physical Review Letters","article_type":"original","article_processing_charge":"No","day":"10","scopus_import":"1","keyword":["General Physics and Astronomy"],"oa_version":"Preprint","_id":"12723","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 130","title":"Spin-electric coupling in lead halide perovskites","status":"public","issue":"10","abstract":[{"text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.","lang":"eng"}],"type":"journal_article","doi":"10.1103/physrevlett.130.106901","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"oa":1,"external_id":{"isi":["000982435900002"],"arxiv":["2203.09443"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03","author":[{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"},{"full_name":"Shiva Kumar, Abhishek","first_name":"Abhishek","last_name":"Shiva Kumar","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc"},{"full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes","last_name":"Ashourishokri"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek"}],"volume":130,"date_created":"2023-03-14T13:11:59Z","date_updated":"2023-08-01T13:39:04Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","article_number":"106901"},{"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.107.125201","month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2023","date_created":"2023-03-14T13:13:05Z","date_updated":"2023-08-01T13:39:47Z","volume":107,"author":[{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek"},{"first_name":"Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"full_name":"Ashourishokri, Younes","first_name":"Younes","last_name":"Ashourishokri","id":"e32c111f-f6e0-11ea-865d-eb955baea334"},{"full_name":"Zhumekenov, Ayan","first_name":"Ayan","last_name":"Zhumekenov"},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"}],"article_number":"125201","article_type":"original","publication":"Physical Review B","citation":{"chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201.","ieee":"A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201"},"date_published":"2023-03-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","status":"public","title":"Effective model for studying optical properties of lead halide perovskites","intvolume":" 107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12724","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"issue":"12"},{"doi":"10.1371/journal.pone.0277148","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001024737400001"]},"oa":1,"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1932-6203"]},"month":"03","author":[{"last_name":"Rothman","first_name":"Jason Seth","full_name":"Rothman, Jason Seth"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina"},{"full_name":"Holderith, Noemi","last_name":"Holderith","first_name":"Noemi"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"first_name":"R.","last_name":"Angus Silver","full_name":"Angus Silver, R."}],"volume":18,"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:46:39Z","year":"2023","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","publisher":"Public Library of Science","department":[{"_id":"PeJo"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-03-27T06:51:09Z","article_number":"e0277148","date_published":"2023-03-17T00:00:00Z","citation":{"apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023.","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148."},"publication":"PLoS ONE","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"17","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":7290413,"creator":"dernst","file_name":"2023_PLoSOne_Rothman.pdf","access_level":"open_access","date_updated":"2023-03-27T06:51:09Z","date_created":"2023-03-27T06:51:09Z","checksum":"2380331ec27cc87808826fc64419ac1c","success":1,"relation":"main_file","file_id":"12770"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12759","intvolume":" 18","status":"public","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","ddc":["570"],"issue":"3 March","abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"type":"journal_article"},{"ddc":["570"],"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","status":"public","intvolume":" 9","_id":"12756","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_name":"2023_ScienceAdvances_Hurtig.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1826471,"file_id":"12768","relation":"main_file","date_updated":"2023-03-27T06:24:49Z","date_created":"2023-03-27T06:24:49Z","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5"}],"type":"journal_article","abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"issue":"11","article_type":"original","publication":"Science Advances","citation":{"ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224","ieee":"F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224."},"date_published":"2023-03-17T00:00:00Z","scopus_import":"1","day":"17","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"AnSa"}],"year":"2023","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","date_updated":"2023-08-01T13:45:54Z","date_created":"2023-03-26T22:01:06Z","volume":9,"author":[{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"full_name":"Burgers, Thomas C.Q.","last_name":"Burgers","first_name":"Thomas C.Q."},{"first_name":"Alice","last_name":"Cezanne","full_name":"Cezanne, Alice"},{"last_name":"Jiang","first_name":"Xiuyun","full_name":"Jiang, Xiuyun"},{"last_name":"Mol","first_name":"Frank N.","full_name":"Mol, Frank N."},{"last_name":"Traparić","first_name":"Jovan","full_name":"Traparić, Jovan"},{"last_name":"Pulschen","first_name":"Andre Arashiro","full_name":"Pulschen, Andre Arashiro"},{"first_name":"Tim","last_name":"Nierhaus","full_name":"Nierhaus, Tim"},{"first_name":"Gabriel","last_name":"Tarrason-Risa","full_name":"Tarrason-Risa, Gabriel"},{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"first_name":"Jan","last_name":"Löwe","full_name":"Löwe, Jan"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Vlijm, Rifka","first_name":"Rifka","last_name":"Vlijm"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"}],"article_number":"eade5224","file_date_updated":"2023-03-27T06:24:49Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000968083500010"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.ade5224","month":"03","publication_identifier":{"eissn":["2375-2548"]}},{"date_published":"2023-03-16T00:00:00Z","citation":{"ieee":"M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689."},"publication":"PLoS ONE","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","oa_version":"Published Version","file":[{"success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","date_created":"2023-03-27T07:09:08Z","date_updated":"2023-03-27T07:09:08Z","file_id":"12771","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":856625,"access_level":"open_access","file_name":"2023_PLoSOne_Pak.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12758","intvolume":" 18","ddc":["570"],"status":"public","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","issue":"3","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"type":"journal_article","doi":"10.1371/journal.pone.0282689","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000985134400106"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1932-6203"]},"month":"03","author":[{"full_name":"Pak, Marina A.","last_name":"Pak","first_name":"Marina A."},{"last_name":"Markhieva","first_name":"Karina A.","full_name":"Markhieva, Karina A."},{"first_name":"Mariia S.","last_name":"Novikova","full_name":"Novikova, Mariia S."},{"first_name":"Dmitry S.","last_name":"Petrov","full_name":"Petrov, Dmitry S."},{"full_name":"Vorobyev, Ilya S.","first_name":"Ilya S.","last_name":"Vorobyev"},{"first_name":"Ekaterina","last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","full_name":"Maksimova, Ekaterina"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N.","last_name":"Ivankov","first_name":"Dmitry N."}],"volume":18,"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:47:14Z","year":"2023","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"publisher":"Public Library of Science","publication_status":"published","file_date_updated":"2023-03-27T07:09:08Z","article_number":"e0282689"},{"author":[{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"volume":480,"date_updated":"2023-08-01T13:45:12Z","date_created":"2023-03-26T22:01:06Z","pmid":1,"year":"2023","department":[{"_id":"LeSa"}],"publisher":"Portland Press","publication_status":"published","publication_identifier":{"eissn":["1470-8728"],"issn":["0264-6021"]},"month":"03","doi":"10.1042/BCJ20210285","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1042/BCJ20210285"}],"external_id":{"isi":["000957065700001"],"pmid":["36920092"]},"isi":1,"quality_controlled":"1","issue":"5","abstract":[{"lang":"eng","text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues."}],"type":"journal_article","oa_version":"Published Version","_id":"12757","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 480","title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","status":"public","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2023-03-15T00:00:00Z","citation":{"ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285."},"publication":"The Biochemical Journal","page":"319-333","article_type":"review"},{"oa_version":"Published Version","file":[{"file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":827784,"file_id":"12796","relation":"main_file","date_created":"2023-04-03T06:25:29Z","date_updated":"2023-04-03T06:25:29Z","success":1,"checksum":"13953d349fbefcb5d21ccc6b303297eb"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12787","intvolume":" 479","status":"public","title":"Coexistence times in the Moran process with environmental heterogeneity","ddc":["000"],"issue":"2271","abstract":[{"text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-29T00:00:00Z","citation":{"ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685."},"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"29","scopus_import":"1","related_material":{"link":[{"relation":"research_data","url":"https://doi.org/10.6084/m9.figshare.21261771.v1"}]},"author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"},{"full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec"},{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"volume":479,"date_created":"2023-04-02T22:01:09Z","date_updated":"2023-08-01T13:58:34Z","acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","year":"2023","publisher":"The Royal Society","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-04-03T06:25:29Z","article_number":"20220685","doi":"10.1098/rspa.2022.0685","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000957125500002"]},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]},"month":"03"},{"date_published":"2023-03-10T00:00:00Z","citation":{"mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.","ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","apa":"Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023."},"publication":"Physical Review Letters","article_type":"original","article_processing_charge":"No","day":"10","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12788","intvolume":" 130","status":"public","title":"Topological charges of periodically kicked molecules","issue":"10","abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}],"type":"journal_article","doi":"10.1103/PhysRevLett.130.103202","language":[{"iso":"eng"}],"external_id":{"isi":["000957635500003"],"arxiv":["2206.07067"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.07067","open_access":"1"}],"project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03","related_material":{"link":[{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/"}]},"author":[{"full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","first_name":"Volker"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"volume":130,"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T14:02:06Z","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"article_number":"103202"},{"oa_version":"Preprint","_id":"12790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","status":"public","intvolume":" 107","abstract":[{"text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2023-03-01T00:00:00Z","publication":"Physical Review B","citation":{"short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502","ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023.","apa":"Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"full_name":"Berg, Erez","last_name":"Berg","first_name":"Erez"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"related_material":{"link":[{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/"}]},"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T13:59:29Z","volume":107,"acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","year":"2023","publication_status":"published","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publisher":"American Physical Society","article_number":"104502","doi":"10.1103/PhysRevB.107.104502","language":[{"iso":"eng"}],"external_id":{"isi":["000945526400003"],"arxiv":["2211.02492"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.02492"}],"oa":1,"quality_controlled":"1","isi":1,"month":"03","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]}},{"day":"20","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-20T00:00:00Z","publication":"The European Physical Journal E","citation":{"chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9","ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023.","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9"},"article_type":"original","abstract":[{"text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","_id":"12791","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","intvolume":" 46","month":"03","publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"doi":"10.1140/epje/s10189-023-00276-9","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2301.07769"}],"external_id":{"isi":["000956387200001"],"arxiv":["2301.07769"]},"oa":1,"isi":1,"quality_controlled":"1","article_number":"16","author":[{"full_name":"Clark Di Leoni, Patricio","first_name":"Patricio","last_name":"Clark Di Leoni"},{"last_name":"Agasthya","first_name":"Lokahith N","id":"cd100965-0804-11ed-9c55-f4878ff4e877","full_name":"Agasthya, Lokahith N"},{"full_name":"Buzzicotti, Michele","first_name":"Michele","last_name":"Buzzicotti"},{"first_name":"Luca","last_name":"Biferale","full_name":"Biferale, Luca"}],"date_created":"2023-04-02T22:01:11Z","date_updated":"2023-08-01T14:03:47Z","volume":46,"acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","year":"2023","publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"Springer Nature"},{"ec_funded":1,"file_date_updated":"2023-04-17T07:41:25Z","volume":58,"date_created":"2023-04-16T22:01:07Z","date_updated":"2023-08-01T14:10:38Z","author":[{"full_name":"Huljev, Karla","first_name":"Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"last_name":"Nunes Pinheiro","first_name":"Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C"},{"last_name":"Preusser","first_name":"Friedrich","full_name":"Preusser, Friedrich"},{"full_name":"Steccari, Irene","last_name":"Steccari","first_name":"Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"first_name":"Suyash","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication_status":"published","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","year":"2023","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"month":"04","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"doi":"10.1016/j.devcel.2023.02.016","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000982111800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"7","abstract":[{"lang":"eng","text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_DevelopmentalCell_Huljev.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7925886,"creator":"dernst","relation":"main_file","file_id":"12842","date_created":"2023-04-17T07:41:25Z","date_updated":"2023-04-17T07:41:25Z","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","success":1}],"intvolume":" 58","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","ddc":["570"],"status":"public","_id":"12830","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"10","scopus_import":"1","date_published":"2023-04-10T00:00:00Z","page":"582-596.e7","article_type":"original","citation":{"ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016."},"publication":"Developmental Cell"},{"doi":"10.1063/5.0135893","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2211.08070"],"isi":["000970038800001"]},"project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"]},"month":"04","author":[{"last_name":"Zeng","first_name":"Zhongda","full_name":"Zeng, Zhongda"},{"full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","first_name":"Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"first_name":"Tao","last_name":"Shi","full_name":"Shi, Tao"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"}],"volume":158,"date_updated":"2023-08-01T14:08:47Z","date_created":"2023-04-16T22:01:07Z","year":"2023","acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","publisher":"American Institute of Physics","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-04-17T07:28:38Z","article_number":"134301","date_published":"2023-04-07T00:00:00Z","citation":{"apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” The Journal of Chemical Physics, vol. 158, no. 13. American Institute of Physics, 2023.","ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301.","ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13). doi:10.1063/5.0135893","chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:10.1063/5.0135893."},"publication":"The Journal of Chemical Physics","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":7388057,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_JourChemicalPhysics_Zeng.pdf","checksum":"8d801babea4df48e08895c76571bb19e","success":1,"date_updated":"2023-04-17T07:28:38Z","date_created":"2023-04-17T07:28:38Z","relation":"main_file","file_id":"12841"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12831","intvolume":" 158","title":"Variational theory of angulons and their rotational spectroscopy","status":"public","ddc":["530"],"issue":"13","abstract":[{"lang":"eng","text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions."}],"type":"journal_article"},{"type":"journal_article","issue":"1","abstract":[{"text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.","lang":"eng"}],"_id":"12839","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 13","ddc":["530"],"status":"public","title":"Superdiffusive energy transport in kinetically constrained models","oa_version":"Published Version","file":[{"date_updated":"2023-04-17T08:36:53Z","date_created":"2023-04-17T08:36:53Z","checksum":"ee060cea609af79bba7af74b1ce28078","success":1,"relation":"main_file","file_id":"12845","file_size":1958523,"content_type":"application/pdf","creator":"dernst","file_name":"2023_PhysReviewX_Ljubotina.pdf","access_level":"open_access"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","citation":{"chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.","mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:10.1103/PhysRevX.13.011033.","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033.","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” Physical Review X, vol. 13, no. 1. American Physical Society, 2023.","ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033"},"publication":"Physical Review X","article_type":"original","date_published":"2023-03-07T00:00:00Z","article_number":"011033","ec_funded":1,"file_date_updated":"2023-04-17T08:36:53Z","acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","year":"2023","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","author":[{"full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko"},{"full_name":"Desaules, Jean Yves","last_name":"Desaules","first_name":"Jean Yves"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"volume":13,"date_created":"2023-04-16T22:01:09Z","date_updated":"2023-08-01T14:11:28Z","publication_identifier":{"eissn":["2160-3308"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000957625700001"]},"oa":1,"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevX.13.011033","language":[{"iso":"eng"}]},{"page":"287-298","article_type":"original","citation":{"ama":"He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 2023;58(4):287-298. doi:10.1016/j.ensm.2023.03.022","ieee":"R. He et al., “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” Energy Storage Materials, vol. 58, no. 4. Elsevier, pp. 287–298, 2023.","apa":"He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. Elsevier. https://doi.org/10.1016/j.ensm.2023.03.022","ista":"He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298.","short":"R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298.","mla":"He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:10.1016/j.ensm.2023.03.022.","chicago":"He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials. Elsevier, 2023. https://doi.org/10.1016/j.ensm.2023.03.022."},"publication":"Energy Storage Materials","date_published":"2023-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 58","status":"public","title":"A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance","_id":"12832","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","type":"journal_article","issue":"4","abstract":[{"text":"The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2.","lang":"eng"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000967601700001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1016/j.ensm.2023.03.022","publication_identifier":{"eissn":["2405-8297"]},"month":"04","publisher":"Elsevier","department":[{"_id":"MaIb"}],"publication_status":"published","year":"2023","acknowledgement":"The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).","volume":58,"date_updated":"2023-08-01T14:08:02Z","date_created":"2023-04-16T22:01:07Z","author":[{"first_name":"Ren","last_name":"He","full_name":"He, Ren"},{"full_name":"Yang, Linlin","last_name":"Yang","first_name":"Linlin"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Wang, Xiang","last_name":"Wang","first_name":"Xiang"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho"},{"full_name":"Zhang, Ting","last_name":"Zhang","first_name":"Ting"},{"first_name":"Lingxiao","last_name":"Li","full_name":"Li, Lingxiao"},{"first_name":"Zhifu","last_name":"Liang","full_name":"Liang, Zhifu"},{"first_name":"Jingwei","last_name":"Chen","full_name":"Chen, Jingwei"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"last_name":"Ostovari Moghaddam","first_name":"Ahmad","full_name":"Ostovari Moghaddam, Ahmad"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Ying","last_name":"Xu","full_name":"Xu, Ying"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129.","mla":"Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129, Wiley, 2023, doi:10.1002/aisy.202200129.","short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.","ieee":"Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” Advanced Intelligent Systems, vol. 5, no. 1. Wiley, 2023.","apa":"Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. Wiley. https://doi.org/10.1002/aisy.202200129","ama":"Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129"},"publication":"Advanced Intelligent Systems","article_type":"original","date_published":"2023-01-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter.","lang":"eng"}],"_id":"12822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 5","title":"Rotation control, interlocking, and self‐positioning of active cogwheels","ddc":["530"],"status":"public","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2414125,"access_level":"open_access","file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","success":1,"checksum":"d48fc41d39892e7fa0d44cb352dd46aa","date_updated":"2023-04-17T06:44:17Z","date_created":"2023-04-17T06:44:17Z","file_id":"12840","relation":"main_file"}],"publication_identifier":{"issn":["2640-4567"]},"month":"01","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2201.03333"],"isi":["000852291200001"]},"quality_controlled":"1","isi":1,"doi":"10.1002/aisy.202200129","language":[{"iso":"eng"}],"article_number":"2200129","file_date_updated":"2023-04-17T06:44:17Z","acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","year":"2023","department":[{"_id":"JePa"}],"publisher":"Wiley","publication_status":"published","author":[{"id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","first_name":"Quentin","last_name":"Martinet","full_name":"Martinet, Quentin"},{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A"}],"volume":5,"date_updated":"2023-08-01T14:06:50Z","date_created":"2023-04-12T08:30:03Z"},{"date_published":"2023-03-24T00:00:00Z","article_type":"original","citation":{"ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2","chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2."},"publication":"Nature Communications","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","file":[{"date_updated":"2023-04-11T06:27:00Z","date_created":"2023-04-11T06:27:00Z","success":1,"checksum":"54f06f9eee11d43bab253f3492c983ba","file_id":"12821","relation":"main_file","creator":"dernst","file_size":4146777,"content_type":"application/pdf","file_name":"2023_NatureComm_Brandstaetter.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 14","status":"public","title":"Curvature induces active velocity waves in rotating spherical tissues","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12818","abstract":[{"lang":"eng","text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37054-2","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"publication_identifier":{"eissn":["2041-1723"]},"month":"03","volume":14,"date_created":"2023-04-09T22:01:00Z","date_updated":"2023-08-01T14:05:30Z","author":[{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"full_name":"Han, Yu Long","last_name":"Han","first_name":"Yu Long"},{"last_name":"Alert","first_name":"Ricard","full_name":"Alert, Ricard"},{"last_name":"Guo","first_name":"Ming","full_name":"Guo, Ming"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","file_date_updated":"2023-04-11T06:27:00Z","article_number":"1643"},{"issue":"3","abstract":[{"lang":"eng","text":"Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds."}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12819","intvolume":" 107","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","status":"public","article_processing_charge":"No","day":"22","scopus_import":"1","date_published":"2023-03-22T00:00:00Z","citation":{"short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023).","mla":"Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.","chicago":"Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L031701.","ama":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701","apa":"Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L031701","ieee":"A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical Society, 2023.","ista":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701."},"publication":"Physical Review A","article_type":"letter_note","article_number":"L031701","author":[{"full_name":"Sokolova, Alesya","orcid":"0000-0002-8308-4144","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","last_name":"Sokolova","first_name":"Alesya"},{"last_name":"Kalacheva","first_name":"D. A.","full_name":"Kalacheva, D. A."},{"full_name":"Fedorov, G. P.","first_name":"G. P.","last_name":"Fedorov"},{"last_name":"Astafiev","first_name":"O. V.","full_name":"Astafiev, O. V."}],"volume":107,"date_created":"2023-04-09T22:01:00Z","date_updated":"2023-08-01T14:06:05Z","acknowledgement":"We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026.","year":"2023","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"month":"03","doi":"10.1103/PhysRevA.107.L031701","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.05165","open_access":"1"}],"external_id":{"arxiv":["2209.05165"],"isi":["000957799000006"]},"quality_controlled":"1","isi":1},{"publication_identifier":{"eissn":["2041-1723"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37817-x","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001003644100020"],"pmid":["37045828"]},"oa":1,"ec_funded":1,"file_date_updated":"2023-04-25T09:13:53Z","article_number":"2086","volume":14,"date_created":"2023-04-23T22:01:03Z","date_updated":"2023-08-01T14:15:57Z","author":[{"full_name":"Schmid, Laura","last_name":"Schmid","first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ekbatani","first_name":"Farbod","full_name":"Ekbatani, Farbod"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","article_processing_charge":"No","has_accepted_license":"1","day":"12","scopus_import":"1","date_published":"2023-04-12T00:00:00Z","article_type":"original","citation":{"ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 2023;14. doi:10.1038/s41467-023-37817-x","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.","mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer Nature, 2023, doi:10.1038/s41467-023-37817-x.","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023)."},"publication":"Nature Communications","abstract":[{"lang":"eng","text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_NatureComm_Schmid.pdf","creator":"dernst","content_type":"application/pdf","file_size":1786475,"file_id":"12868","relation":"main_file","success":1,"checksum":"a4b3b7b36fbef068cabf4fb99501fef6","date_updated":"2023-04-25T09:13:53Z","date_created":"2023-04-25T09:13:53Z"}],"oa_version":"Published Version","intvolume":" 14","status":"public","title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12861"},{"file_date_updated":"2023-04-25T08:59:18Z","article_number":"e1010983","volume":19,"date_updated":"2023-08-01T14:15:16Z","date_created":"2023-04-23T22:01:03Z","related_material":{"link":[{"url":"https://github.com/shervinsafavi/gpla.git","relation":"software"}]},"author":[{"first_name":"Shervin","last_name":"Safavi","full_name":"Safavi, Shervin"},{"last_name":"Panagiotaropoulos","first_name":"Theofanis I.","full_name":"Panagiotaropoulos, Theofanis I."},{"last_name":"Kapoor","first_name":"Vishal","full_name":"Kapoor, Vishal"},{"full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F","last_name":"Ramirez Villegas"},{"first_name":"Nikos K.","last_name":"Logothetis","full_name":"Logothetis, Nikos K."},{"full_name":"Besserve, Michel","first_name":"Michel","last_name":"Besserve"}],"publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"publication_status":"published","year":"2023","acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","publication_identifier":{"eissn":["1553-7358"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1010983","quality_controlled":"1","isi":1,"external_id":{"isi":["000962668700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"4","abstract":[{"text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-04-25T08:59:18Z","date_created":"2023-04-25T08:59:18Z","success":1,"checksum":"edeb9d09f3e41ba7c0251308b9e372e7","file_id":"12867","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4737671,"file_name":"2023_PLoSCompBio_Safavi.pdf","access_level":"open_access"}],"intvolume":" 19","ddc":["570"],"status":"public","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12862","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","article_type":"original","citation":{"chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol. 19, no. 4. Public Library of Science, 2023.","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983","ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983"},"publication":"PLoS Computational Biology"},{"date_created":"2023-04-30T22:01:06Z","date_updated":"2023-08-01T14:18:10Z","author":[{"id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","last_name":"Chen","first_name":"Ke","full_name":"Chen, Ke"},{"full_name":"Kunkel, Christian","first_name":"Christian","last_name":"Kunkel"},{"full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"last_name":"Reuter","first_name":"Karsten","full_name":"Reuter, Karsten"},{"full_name":"Margraf, Johannes T.","last_name":"Margraf","first_name":"Johannes T."}],"publication_status":"published","department":[{"_id":"BiCh"}],"publisher":"Royal Society of Chemistry","acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","year":"2023","license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2023-05-02T07:17:05Z","language":[{"iso":"eng"}],"doi":"10.1039/d3sc00841j","quality_controlled":"1","isi":1,"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000971508100001"]},"month":"04","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"oa_version":"Published Version","file":[{"date_created":"2023-05-02T07:17:05Z","date_updated":"2023-05-02T07:17:05Z","checksum":"5eeec69a51e192dcd94b955d84423836","success":1,"relation":"main_file","file_id":"12883","file_size":1515446,"content_type":"application/pdf","creator":"dernst","file_name":"2023_ChemialScience_Chen.pdf","access_level":"open_access"}],"title":"Physics-inspired machine learning of localized intensive properties","ddc":["000","540"],"status":"public","_id":"12879","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.","lang":"eng"}],"type":"journal_article","date_published":"2023-04-10T00:00:00Z","article_type":"original","publication":"Chemical Science","citation":{"ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” Chemical Science. Royal Society of Chemistry, 2023.","apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d3sc00841j","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j."},"day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12878","intvolume":" 115","status":"public","title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal. Wiley, 2023. https://doi.org/10.1111/tpj.16218.","mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218.","short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218","ieee":"L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal, vol. 115, no. 1. Wiley, pp. 155–174, 2023.","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 2023;115(1):155-174. doi:10.1111/tpj.16218"},"publication":"Plant Journal","page":"155-174","article_type":"original","date_published":"2023-07-01T00:00:00Z","pmid":1,"acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","year":"2023","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Jiang, Lihui","last_name":"Jiang","first_name":"Lihui"},{"full_name":"Yao, Baolin","last_name":"Yao","first_name":"Baolin"},{"first_name":"Xiaoyan","last_name":"Zhang","full_name":"Zhang, Xiaoyan"},{"last_name":"Wu","first_name":"Lixia","full_name":"Wu, Lixia"},{"last_name":"Fu","first_name":"Qijing","full_name":"Fu, Qijing"},{"full_name":"Zhao, Yiting","first_name":"Yiting","last_name":"Zhao"},{"last_name":"Cao","first_name":"Yuxin","full_name":"Cao, Yuxin"},{"full_name":"Zhu, Ruomeng","first_name":"Ruomeng","last_name":"Zhu"},{"full_name":"Lu, Xinqi","first_name":"Xinqi","last_name":"Lu"},{"first_name":"Wuying","last_name":"Huang","full_name":"Huang, Wuying"},{"full_name":"Zhao, Jianping","first_name":"Jianping","last_name":"Zhao"},{"full_name":"Li, Kuixiu","first_name":"Kuixiu","last_name":"Li"},{"last_name":"Zhao","first_name":"Shuanglu","full_name":"Zhao, Shuanglu"},{"last_name":"Han","first_name":"Li","full_name":"Han, Li"},{"full_name":"Zhou, Xuan","last_name":"Zhou","first_name":"Xuan"},{"first_name":"Chongyu","last_name":"Luo","full_name":"Luo, Chongyu"},{"last_name":"Zhu","first_name":"Haiyan","full_name":"Zhu, Haiyan"},{"last_name":"Yang","first_name":"Jing","full_name":"Yang, Jing"},{"first_name":"Huichuan","last_name":"Huang","full_name":"Huang, Huichuan"},{"first_name":"Zhengge","last_name":"Zhu","full_name":"Zhu, Zhengge"},{"full_name":"He, Xiahong","first_name":"Xiahong","last_name":"He"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zhongkai","last_name":"Zhang","full_name":"Zhang, Zhongkai"},{"full_name":"Liu, Changning","last_name":"Liu","first_name":"Changning"},{"full_name":"Du, Yunlong","last_name":"Du","first_name":"Yunlong"}],"volume":115,"date_created":"2023-04-30T22:01:06Z","date_updated":"2023-08-01T14:16:33Z","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"month":"07","external_id":{"isi":["000971861400001"],"pmid":["37025008 "]},"quality_controlled":"1","isi":1,"doi":"10.1111/tpj.16218","language":[{"iso":"eng"}]},{"file_date_updated":"2023-05-02T07:39:04Z","ec_funded":1,"article_number":"btad158","author":[{"full_name":"Beneš, Nikola","first_name":"Nikola","last_name":"Beneš"},{"first_name":"Luboš","last_name":"Brim","full_name":"Brim, Luboš"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"first_name":"Samuel","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel"},{"last_name":"Šafránek","first_name":"David","full_name":"Šafránek, David"}],"related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.7688740"}]},"date_updated":"2023-08-01T14:27:28Z","date_created":"2023-04-30T22:01:05Z","volume":39,"acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","year":"2023","pmid":1,"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"ToHe"}],"month":"04","publication_identifier":{"eissn":["1367-4811"]},"doi":"10.1093/bioinformatics/btad158","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"quality_controlled":"1","isi":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"abstract":[{"text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12886","checksum":"2cb90ddf781baefddf47eac4b54e2a03","success":1,"date_created":"2023-05-02T07:39:04Z","date_updated":"2023-05-02T07:39:04Z","access_level":"open_access","file_name":"2023_Bioinformatics_Benes.pdf","file_size":478740,"content_type":"application/pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12876","ddc":["000"],"title":"Boolean network sketches: A unifying framework for logical model inference","status":"public","intvolume":" 39","day":"03","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-03T00:00:00Z","publication":"Bioinformatics","citation":{"ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” Bioinformatics, vol. 39, no. 4. Oxford Academic, 2023.","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 2023;39(4). doi:10.1093/bioinformatics/btad158","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.","mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:10.1093/bioinformatics/btad158.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023)."},"article_type":"original"},{"day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-18T00:00:00Z","publication":"Nucleus","citation":{"ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548","apa":"Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. Taylor & Francis. https://doi.org/10.1080/19491034.2023.2202548","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” Nucleus, vol. 14, no. 1. Taylor & Francis, 2023.","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis, 2023, doi:10.1080/19491034.2023.2202548.","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus. Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548."},"article_type":"original","abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12884","relation":"main_file","success":1,"checksum":"8e707eda84f64dbad7f03545ae0a83ef","date_updated":"2023-05-02T07:24:55Z","date_created":"2023-05-02T07:24:55Z","access_level":"open_access","file_name":"2023_Nucleus_Kaneshiro.pdf","creator":"dernst","content_type":"application/pdf","file_size":3811113}],"_id":"12880","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Lamin B1 overexpression alters chromatin organization and gene expression","ddc":["570"],"intvolume":" 14","month":"04","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"doi":"10.1080/19491034.2023.2202548","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000971629400001"],"pmid":["37071033"]},"isi":1,"quality_controlled":"1","file_date_updated":"2023-05-02T07:24:55Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"2202548","author":[{"full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro","first_name":"Jeanae M."},{"first_name":"Juliana S.","last_name":"Capitanio","full_name":"Capitanio, Juliana S."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"Hetzer","full_name":"Hetzer, Martin W"}],"date_updated":"2023-08-01T14:18:46Z","date_created":"2023-04-30T22:01:06Z","volume":14,"year":"2023","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","pmid":1,"publication_status":"published","department":[{"_id":"MaHe"}],"publisher":"Taylor & Francis"},{"article_number":"042216","ec_funded":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","year":"2023","date_created":"2023-05-07T22:01:03Z","date_updated":"2023-08-01T14:33:21Z","volume":107,"author":[{"full_name":"Suzuki, Fumika","last_name":"Suzuki","first_name":"Fumika","orcid":"0000-0003-4982-5970","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E"},{"full_name":"Unruh, William G.","first_name":"William G.","last_name":"Unruh"}],"month":"04","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"isi":["000975799300006"],"arxiv":["2207.13130"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.13130","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.042216","type":"journal_article","abstract":[{"lang":"eng","text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier."}],"issue":"4","title":"Numerical quantum clock simulations for measuring tunneling times","status":"public","intvolume":" 107","_id":"12914","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","day":"20","article_processing_charge":"No","article_type":"original","publication":"Physical Review A","citation":{"chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.","apa":"Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.042216","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” Physical Review A, vol. 107, no. 4. American Physical Society, 2023.","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","ama":"Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216"},"date_published":"2023-04-20T00:00:00Z"},{"abstract":[{"text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1405588,"creator":"dernst","file_name":"2023_NatureComm_DiezMerida.pdf","access_level":"open_access","date_updated":"2023-05-08T07:26:40Z","date_created":"2023-05-08T07:26:40Z","checksum":"a778105665c10beb2354c92d2b295115","success":1,"relation":"main_file","file_id":"12917"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12913","title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","status":"public","ddc":["530"],"intvolume":" 14","day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-26T00:00:00Z","publication":"Nature Communications","citation":{"mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications, vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.","short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023).","chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.","ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 2023;14. doi:10.1038/s41467-023-38005-7","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396.","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38005-7","ieee":"J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” Nature Communications, vol. 14. Springer Nature, 2023."},"article_type":"original","file_date_updated":"2023-05-08T07:26:40Z","article_number":"2396","author":[{"full_name":"Díez-Mérida, J.","first_name":"J.","last_name":"Díez-Mérida"},{"full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón","first_name":"A."},{"last_name":"Yang","first_name":"S. Y.","full_name":"Yang, S. Y."},{"full_name":"Xie, Y. M.","first_name":"Y. M.","last_name":"Xie"},{"first_name":"X. J.","last_name":"Gao","full_name":"Gao, X. J."},{"first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L"},{"last_name":"Watanabe","first_name":"K.","full_name":"Watanabe, K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"full_name":"Lu, X.","last_name":"Lu","first_name":"X."},{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"},{"first_name":"K. T.","last_name":"Law","full_name":"Law, K. T."},{"full_name":"Efetov, Dmitri K.","last_name":"Efetov","first_name":"Dmitri K."}],"date_updated":"2023-08-01T14:34:00Z","date_created":"2023-05-07T22:01:03Z","volume":14,"acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","year":"2023","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"AnHi"}],"month":"04","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-38005-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37100775"],"isi":["000979744000004"]},"isi":1,"quality_controlled":"1"},{"article_type":"original","citation":{"ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.","apa":"Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66.","ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w."},"publication":"Journal of Nonlinear Science","date_published":"2023-06-07T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"07","intvolume":" 33","status":"public","ddc":["510"],"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10550","file":[{"content_type":"application/pdf","file_size":742315,"creator":"dernst","file_name":"2023_JourNonlinearScience_Fellner.pdf","access_level":"open_access","date_created":"2023-06-19T07:33:53Z","date_updated":"2023-06-19T07:33:53Z","checksum":"f3f0f0886098e31c81116cff8183750b","success":1,"relation":"main_file","file_id":"13149"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter."}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00332-023-09926-w","publication_identifier":{"eissn":["1432-1467"],"issn":["0938-8974"]},"month":"06","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","year":"2023","volume":33,"date_updated":"2023-08-01T14:40:33Z","date_created":"2021-12-16T12:15:35Z","author":[{"full_name":"Fellner, Klemens","last_name":"Fellner","first_name":"Klemens"},{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L"},{"full_name":"Kniely, Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","first_name":"Michael","last_name":"Kniely"},{"full_name":"Tang, Bao Quoc","last_name":"Tang","first_name":"Bao Quoc"}],"article_number":"66","file_date_updated":"2023-06-19T07:33:53Z"},{"publication_identifier":{"eissn":["1463-9971"],"issn":["1463-9963"]},"month":"04","project":[{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2108.01733"],"isi":["000975817300002"]},"language":[{"iso":"eng"}],"doi":"10.4171/IFB/484","ec_funded":1,"file_date_updated":"2023-05-22T07:24:13Z","department":[{"_id":"JuFi"}],"publisher":"EMS Press","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","year":"2023","volume":25,"date_created":"2023-05-21T22:01:06Z","date_updated":"2023-08-01T14:43:29Z","related_material":{"record":[{"id":"10013","status":"public","relation":"earlier_version"}]},"author":[{"orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel","first_name":"Sebastian","full_name":"Hensel, Sebastian"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","page":"37-107","article_type":"original","citation":{"mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1, EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484.","short":"S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023. https://doi.org/10.4171/IFB/484.","ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484","ista":"Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.","ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS Press, pp. 37–107, 2023.","apa":"Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484"},"publication":"Interfaces and Free Boundaries","date_published":"2023-04-20T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction\r\nof a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting along triple junctions."}],"intvolume":" 25","title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","ddc":["510"],"status":"public","_id":"13043","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","file_name":"2023_Interfaces_Hensel.pdf","file_size":867876,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13045","checksum":"622422484810441e48f613e968c7e7a4","success":1,"date_created":"2023-05-22T07:24:13Z","date_updated":"2023-05-22T07:24:13Z"}],"oa_version":"Published Version"},{"publisher":"AIP Publishing","department":[{"_id":"BiCh"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.","year":"2023","volume":158,"date_created":"2023-05-07T22:01:03Z","date_updated":"2023-08-01T14:34:49Z","related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/mu-adsorption"},{"url":"https://github.com/BingqingCheng/S0","relation":"software"}]},"author":[{"first_name":"Rochus","last_name":"Schmid","full_name":"Schmid, Rochus"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"article_number":"161101 ","file_date_updated":"2023-05-08T07:44:49Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001010676000010"],"pmid":["37093149"],"arxiv":["2302.01297"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0146711","publication_identifier":{"eissn":["1089-7690"]},"month":"04","intvolume":" 158","ddc":["540"],"title":"Computing chemical potentials of adsorbed or confined fluids","status":"public","_id":"12912","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"12918","relation":"main_file","date_updated":"2023-05-08T07:44:49Z","date_created":"2023-05-08T07:44:49Z","success":1,"checksum":"4ab8c965f2fa4e17920bfa846847f137","file_name":"2023_JourChemicalPhysics_Schmid.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":6499468}],"oa_version":"Published Version","type":"journal_article","issue":"16","abstract":[{"text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.","lang":"eng"}],"article_type":"original","citation":{"chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0146711.","mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:10.1063/5.0146711.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing, 2023.","apa":"Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711","ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711"},"publication":"The Journal of Chemical Physics","date_published":"2023-04-24T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"24"},{"ec_funded":1,"file_date_updated":"2023-05-16T08:28:37Z","author":[{"orcid":"0000-0001-9200-5690","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","last_name":"Liu","first_name":"Zhenyuan","full_name":"Liu, Zhenyuan"},{"first_name":"Michael","last_name":"Piovarci","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael"},{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","first_name":"Christian","full_name":"Hafner, Christian"},{"full_name":"Charrondiere, Raphael","first_name":"Raphael","last_name":"Charrondiere","id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"volume":42,"date_updated":"2023-08-01T14:47:05Z","date_created":"2023-05-16T08:47:25Z","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and Paola Mejia for proofreading; everyone in the visual computing group at ISTA for inspiring lunch and coffee breaks; Thibault Tricard for help producing the results of Phasor Noise.","year":"2023","publisher":"Wiley","department":[{"_id":"BeBi"}],"publication_status":"published","publication_identifier":{"issn":["1467-8659"]},"month":"05","doi":"10.1111/cgf.14770 ","conference":{"name":"EG: Eurographics","location":"Saarbrucken, Germany","start_date":"2023-05-08","end_date":"2023-05-12"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["001000062600033"]},"project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"quality_controlled":"1","isi":1,"issue":"2","abstract":[{"text":"Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12974","checksum":"4c188c2be4745467a8790bbf5d6491aa","success":1,"date_updated":"2023-05-16T08:28:37Z","date_created":"2023-05-16T08:28:37Z","access_level":"open_access","file_name":"Zhenyuan2023.pdf","content_type":"application/pdf","file_size":24003702,"creator":"mpiovarc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12972","intvolume":" 42","ddc":["004"],"title":"Directionality-aware design of embroidery patterns","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"08","keyword":["embroidery","design","directionality","density","image"],"date_published":"2023-05-08T00:00:00Z","citation":{"mla":"Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 .","short":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409.","chicago":"Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere, and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770 .","ama":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409. doi:10.1111/cgf.14770 ","ista":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409.","apa":"Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023). Directionality-aware design of embroidery patterns. Computer Graphics Forum. Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770 ","ieee":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2. Wiley, pp. 397–409, 2023."},"publication":"Computer Graphics Forum","page":"397-409","article_type":"original"},{"scopus_import":"1","keyword":["Multidisciplinary"],"article_processing_charge":"No","has_accepted_license":"1","day":"17","citation":{"ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., & Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z.","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023)."},"publication":"Scientific Reports","article_type":"original","date_published":"2023-05-17T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases."}],"_id":"13033","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 13","ddc":["570"],"title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","status":"public","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3055077,"creator":"dernst","file_name":"2023_ScientificReports_Zavadakova.pdf","access_level":"open_access","date_created":"2023-05-22T07:57:37Z","date_updated":"2023-05-22T07:57:37Z","checksum":"8c1b769693ff4288df8376e59ad1176d","success":1,"relation":"main_file","file_id":"13047"}],"publication_identifier":{"issn":["2045-2322"]},"month":"05","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000995271600104"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s41598-023-35162-z","language":[{"iso":"eng"}],"article_number":"7959","file_date_updated":"2023-05-22T07:57:37Z","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","year":"2023","department":[{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-023-37265-z","relation":"erratum"}]},"author":[{"last_name":"Zavadakova","first_name":"Anna","full_name":"Zavadakova, Anna"},{"full_name":"Vistejnova, Lucie","last_name":"Vistejnova","first_name":"Lucie"},{"first_name":"Tereza","last_name":"Belinova","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","full_name":"Belinova, Tereza"},{"full_name":"Tichanek, Filip","last_name":"Tichanek","first_name":"Filip"},{"full_name":"Bilikova, Dagmar","last_name":"Bilikova","first_name":"Dagmar"},{"full_name":"Mouton, Peter R.","last_name":"Mouton","first_name":"Peter R."}],"volume":13,"date_updated":"2023-08-01T14:46:06Z","date_created":"2023-05-19T11:12:25Z"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","page":"10700–10711","article_type":"original","citation":{"chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:10.1021/jacs.3c01200.","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” Journal of the American Chemical Society, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c01200","ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200"},"publication":"Journal of the American Chemical Society","date_published":"2023-05-04T00:00:00Z","type":"journal_article","issue":"19","abstract":[{"lang":"eng","text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts."}],"intvolume":" 145","title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","ddc":["540"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13095","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13098","date_updated":"2023-05-30T07:05:28Z","date_created":"2023-05-30T07:05:28Z","checksum":"0758a930ef21c62fc91b14e657479f83","success":1,"file_name":"2023_JACS_Troussicot.pdf","access_level":"open_access","file_size":6719299,"content_type":"application/pdf","creator":"dernst"}],"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"month":"05","isi":1,"quality_controlled":"1","external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/jacs.3c01200","file_date_updated":"2023-05-30T07:05:28Z","department":[{"_id":"PaSc"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","volume":145,"date_updated":"2023-08-01T14:48:09Z","date_created":"2023-05-28T22:01:04Z","related_material":{"record":[{"id":"12820","relation":"research_data","status":"public"}]},"author":[{"first_name":"Laura","last_name":"Troussicot","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","full_name":"Troussicot, Laura"},{"first_name":"Alicia","last_name":"Vallet","full_name":"Vallet, Alicia"},{"full_name":"Molin, Mikael","last_name":"Molin","first_name":"Mikael"},{"full_name":"Burmann, Björn M.","last_name":"Burmann","first_name":"Björn M."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}]},{"citation":{"ama":"Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi:10.37236/11471","ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21.","apa":"Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471","ieee":"M. Anastos, “A note on long cycles in sparse random graphs,” Electronic Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics, 2023.","mla":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics, 2023, doi:10.37236/11471.","short":"M. Anastos, Electronic Journal of Combinatorics 30 (2023).","chicago":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471."},"publication":"Electronic Journal of Combinatorics","article_type":"original","date_published":"2023-05-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13042","intvolume":" 30","title":"A note on long cycles in sparse random graphs","ddc":["510"],"status":"public","file":[{"success":1,"checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","date_created":"2023-05-22T07:43:19Z","date_updated":"2023-05-22T07:43:19Z","file_id":"13046","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":448736,"access_level":"open_access","file_name":"2023_JourCombinatorics_Anastos.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2105.13828"],"isi":["000988285500001"]},"isi":1,"quality_controlled":"1","doi":"10.37236/11471","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1077-8926"]},"month":"05","year":"2023","acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","department":[{"_id":"MaKw"}],"publisher":"Electronic Journal of Combinatorics","publication_status":"published","author":[{"full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos"}],"volume":30,"date_created":"2023-05-21T22:01:05Z","date_updated":"2023-08-01T14:44:52Z","article_number":"P2.21","file_date_updated":"2023-05-22T07:43:19Z"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"citation":{"ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820","chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.","mla":"Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.","short":"P. Schanda, (2023)."},"doi":"10.15479/AT:ISTA:12820","date_published":"2023-04-18T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","month":"04","day":"18","department":[{"_id":"PaSc"}],"publisher":"Institute of Science and Technology Austria","status":"public","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","ddc":["570"],"_id":"12820","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_size":54184807,"content_type":"application/zip","creator":"pschanda","file_name":"data_deposition.zip","access_level":"open_access","date_updated":"2023-04-14T09:39:33Z","date_created":"2023-04-14T09:39:33Z","checksum":"54a619605e44c871214fb0e07b05c6bf","success":1,"relation":"main_file","file_id":"12823"},{"success":1,"checksum":"8dede9fc78399d13144eb05c62bf5750","date_updated":"2023-04-14T09:39:58Z","date_created":"2023-04-14T09:39:58Z","file_id":"12824","relation":"main_file","creator":"pschanda","file_size":4978,"content_type":"application/octet-stream","access_level":"open_access","file_name":"README"}],"date_created":"2023-04-10T05:55:56Z","date_updated":"2023-08-01T14:48:08Z","related_material":{"record":[{"id":"13095","relation":"used_in_publication","status":"public"}]},"contributor":[{"first_name":"Laura","contributor_type":"researcher","last_name":"Troussicot"},{"contributor_type":"researcher","last_name":"Burmann","first_name":"Björn M."}],"author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}],"type":"research_data","file_date_updated":"2023-04-14T09:39:58Z","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript","lang":"eng"}]},{"type":"journal_article","abstract":[{"text":"We calculate reflectivities of dynamically compressed water, water-ethanol mixtures, and ammonia at infrared and optical wavelengths with density functional theory and molecular dynamics simulations. The influence of the exchange-correlation functional on the results is examined in detail. Our findings indicate that the consistent use of the HSE hybrid functional reproduces experimental results much better than the commonly used PBE functional. The HSE functional offers not only a more accurate description of the electronic band gap but also shifts the onset of molecular dissociation in the molecular dynamics simulations to significantly higher pressures. We also highlight the importance of using accurate reference standards in reflectivity experiments and reanalyze infrared and optical reflectivity data from recent experiments. Thus, our combined theoretical and experimental work explains and resolves lingering discrepancies between calculations and measurements for the investigated molecular substances under shock compression.","lang":"eng"}],"issue":"13","_id":"13039","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Ab initio calculation of the reflectivity of molecular fluids under shock compression","intvolume":" 107","oa_version":"None","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Physical Review B","citation":{"mla":"French, Martin, et al. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B, vol. 107, no. 13, 134109, American Physical Society, 2023, doi:10.1103/PhysRevB.107.134109.","short":"M. French, M. Bethkenhagen, A. Ravasio, J.A. Hernandez, Physical Review B 107 (2023).","chicago":"French, Martin, Mandy Bethkenhagen, Alessandra Ravasio, and Jean Alexis Hernandez. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.134109.","ama":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 2023;107(13). doi:10.1103/PhysRevB.107.134109","ista":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. 2023. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 107(13), 134109.","ieee":"M. French, M. Bethkenhagen, A. Ravasio, and J. A. Hernandez, “Ab initio calculation of the reflectivity of molecular fluids under shock compression,” Physical Review B, vol. 107, no. 13. American Physical Society, 2023.","apa":"French, M., Bethkenhagen, M., Ravasio, A., & Hernandez, J. A. (2023). Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.134109"},"article_type":"original","date_published":"2023-04-01T00:00:00Z","article_number":"134109","year":"2023","acknowledgement":"We thank R. Redmer for helpful discussions. M.F. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG) within the FOR 2440. M.B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Skłodowska-Curie actions (xICE Grant No. 894725) and the NOMIS foundation. A.R. and J.-A.H. acknowledge support form the French National Research Agency (ANR) through the projects POMPEI (Grant No. ANR-16-CE31-0008) and SUPER-ICES (Grant No. ANR-15-CE30-008-01). The ab initio calculations were performed at the NorthGerman Supercomputing Alliance (HLRN) facilities. ","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BiCh"}],"author":[{"first_name":"Martin","last_name":"French","full_name":"French, Martin"},{"last_name":"Bethkenhagen","first_name":"Mandy","orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","full_name":"Bethkenhagen, Mandy"},{"full_name":"Ravasio, Alessandra","first_name":"Alessandra","last_name":"Ravasio"},{"full_name":"Hernandez, Jean Alexis","first_name":"Jean Alexis","last_name":"Hernandez"}],"date_created":"2023-05-21T22:01:04Z","date_updated":"2023-08-01T14:45:25Z","volume":107,"month":"04","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"external_id":{"isi":["000974672600001"]},"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevB.107.134109","language":[{"iso":"eng"}]},{"doi":"10.1021/acsami.3c00625","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37141543"],"isi":["000985497900001"]},"quality_controlled":"1","isi":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"month":"05","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"author":[{"first_name":"Bingfei","last_name":"Nan","full_name":"Nan, Bingfei"},{"full_name":"Song, Xuan","last_name":"Song","first_name":"Xuan"},{"first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng"},{"last_name":"Xiao","first_name":"Ke","full_name":"Xiao, Ke"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"full_name":"Yang, Linlin","first_name":"Linlin","last_name":"Yang"},{"full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"full_name":"Lim, Khak Ho","first_name":"Khak Ho","last_name":"Lim"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"date_created":"2023-05-28T22:01:03Z","date_updated":"2023-08-01T14:50:09Z","volume":15,"year":"2023","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). We thank Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X., and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial support from IST Austria.","pmid":1,"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","file_date_updated":"2023-05-30T07:38:44Z","date_published":"2023-05-04T00:00:00Z","publication":"ACS Applied Materials and Interfaces","citation":{"chicago":"Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625.","mla":"Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625.","short":"B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H. Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.","ista":"Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 15(19), 23380–23389.","apa":"Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023). Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625","ieee":"B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,” ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical Society, pp. 23380–23389, 2023.","ama":"Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389. doi:10.1021/acsami.3c00625"},"article_type":"original","page":"23380–23389","day":"04","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":5640829,"creator":"dernst","access_level":"open_access","file_name":"2023_ACSAppliedMaterials_Nan.pdf","checksum":"23893be46763c4c78daacddd019de821","success":1,"date_created":"2023-05-30T07:38:44Z","date_updated":"2023-05-30T07:38:44Z","relation":"main_file","file_id":"13099"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13092","ddc":["540"],"title":"Bottom-up synthesis of SnTe-based thermoelectric composites","status":"public","intvolume":" 15","abstract":[{"text":"There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe.","lang":"eng"}],"issue":"19","type":"journal_article"},{"ec_funded":1,"file_date_updated":"2023-05-30T07:55:31Z","volume":23,"date_created":"2023-05-28T22:01:03Z","date_updated":"2023-08-01T14:51:25Z","author":[{"full_name":"Azadbakht, Ali","first_name":"Ali","last_name":"Azadbakht"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","first_name":"Billie","full_name":"Meadowcroft, Billie"},{"full_name":"Varkevisser, Thijs","last_name":"Varkevisser","first_name":"Thijs"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"department":[{"_id":"AnSa"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.3c00375","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37141427"],"isi":["000985481400001"]},"issue":"10","abstract":[{"lang":"eng","text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states."}],"type":"journal_article","file":[{"creator":"dernst","file_size":3654910,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_NanoLetters_Azadbakht.pdf","success":1,"checksum":"9734d4c617bab3578ef62916b764547a","date_updated":"2023-05-30T07:55:31Z","date_created":"2023-05-30T07:55:31Z","file_id":"13100","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 23","title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","ddc":["540"],"status":"public","_id":"13094","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2023-05-04T00:00:00Z","page":"4267–4273","article_type":"letter_note","citation":{"ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375."},"publication":"Nano Letters"},{"oa":1,"external_id":{"isi":["000986859000001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsaelm.3c00055"}],"quality_controlled":"1","isi":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.1021/acsaelm.3c00055","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["2637-6113"]},"acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). B.N., M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457 and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/. ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges support from the National Natural Science Foundation of China (22208293). This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.","year":"2023","publication_status":"epub_ahead","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","author":[{"full_name":"Nan, Bingfei","last_name":"Nan","first_name":"Bingfei"},{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"last_name":"Xiao","first_name":"Ke","full_name":"Xiao, Ke"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"first_name":"Yong","last_name":"Zuo","full_name":"Zuo, Yong"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_updated":"2023-08-01T14:50:48Z","date_created":"2023-05-28T22:01:03Z","publication":"ACS Applied Electronic Materials","citation":{"apa":"Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023). Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. American Chemical Society. https://doi.org/10.1021/acsaelm.3c00055","ieee":"B. Nan et al., “Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature,” ACS Applied Electronic Materials. American Chemical Society, 2023.","ista":"Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials.","ama":"Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055","chicago":"Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang, Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055.","short":"B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J. Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials (2023).","mla":"Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055."},"article_type":"original","date_published":"2023-05-05T00:00:00Z","scopus_import":"1","day":"05","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13093","status":"public","title":"Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated."}]},{"publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"TiBr"}],"year":"2023","acknowledgement":"The authors are grateful to Paul Nelson, Per Salberger and Jason Starr for useful comments. While working on this paper the first author was supported by EPRSC grant EP/P026710/1. The research was partially conducted during the period the second author served as a Clay Research Fellow, and partially conducted during the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zurich Foundation.","date_created":"2023-05-28T22:01:02Z","date_updated":"2023-08-01T14:51:57Z","volume":17,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"full_name":"Sawin, Will","last_name":"Sawin","first_name":"Will"}],"file_date_updated":"2023-05-30T08:05:22Z","isi":1,"quality_controlled":"1","project":[{"grant_number":"EP-P026710-2","_id":"26A8D266-B435-11E9-9278-68D0E5697425","name":"Between rational and integral points"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000996014700004"],"arxiv":["1810.06882"]},"language":[{"iso":"eng"}],"doi":"10.2140/ant.2023.17.719","month":"04","publication_identifier":{"issn":["1937-0652"],"eissn":["1944-7833"]},"title":"Free rational curves on low degree hypersurfaces and the circle method","ddc":["510"],"status":"public","intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13091","file":[{"file_name":"2023_AlgebraNumberTheory_Browning.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1430719,"creator":"dernst","relation":"main_file","file_id":"13101","date_created":"2023-05-30T08:05:22Z","date_updated":"2023-05-30T08:05:22Z","checksum":"5d5d67b235905650e33cf7065d7583b4","success":1}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle.","lang":"eng"}],"issue":"3","article_type":"original","page":"719-748","publication":"Algebra and Number Theory","citation":{"short":"T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719.","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719.","ama":"Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719","apa":"Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719","ieee":"T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical Sciences Publishers, pp. 719–748, 2023.","ista":"Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 17(3), 719–748."},"date_published":"2023-04-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2023-05-24T00:00:00Z","article_type":"original","citation":{"chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2023-06-06T07:31:20Z","date_updated":"2023-06-06T07:31:20Z","success":1,"checksum":"a857df40f0882859c48a1ff1e2001ec2","file_id":"13123","relation":"main_file","creator":"dernst","file_size":1654389,"content_type":"application/pdf","file_name":"2023_NaturePhysics_Redchenko.pdf","access_level":"open_access"}],"intvolume":" 14","ddc":["530"],"title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","_id":"13117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41467-023-38761-6","project":[{"_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001001099700002"],"arxiv":["2205.03293"]},"publication_identifier":{"eissn":["2041-1723"]},"month":"05","volume":14,"date_updated":"2023-08-02T06:10:26Z","date_created":"2023-06-04T22:01:02Z","related_material":{"record":[{"id":"13124","relation":"research_data","status":"public"}]},"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"full_name":"Poshakinskiy, Alexander V.","last_name":"Poshakinskiy","first_name":"Alexander V."},{"first_name":"Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"first_name":"Alexander N.","last_name":"Poddubny","full_name":"Poddubny, Alexander N."},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"publisher":"Springer Nature","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2023","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","ec_funded":1,"file_date_updated":"2023-06-06T07:31:20Z","article_number":"2998"},{"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"name":"Quantum readout techniques and technologies","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"oa":1,"external_id":{"arxiv":["2301.03315"],"isi":["000996515200004"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.03315","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.adg3812","month":"05","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"JoFi"}],"acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","year":"2023","date_updated":"2023-08-02T06:08:57Z","date_created":"2023-05-31T11:39:24Z","volume":380,"author":[{"first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh"},{"first_name":"Liu","last_name":"Qiu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu"},{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease"},{"full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Minoguchi","first_name":"Y.","full_name":"Minoguchi, Y."},{"full_name":"Rabl, P.","first_name":"P.","last_name":"Rabl"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/"}],"record":[{"id":"13122","status":"public","relation":"research_data"}]},"ec_funded":1,"article_type":"original","page":"718-721","publication":"Science","citation":{"short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:10.1126/science.adg3812.","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science. 2023;380(6646):718-721. doi:10.1126/science.adg3812","ieee":"R. Sahu et al., “Entangling microwaves with light,” Science, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., & Fink, J. M. (2023). Entangling microwaves with light. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812","ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721."},"date_published":"2023-05-18T00:00:00Z","keyword":["Multidisciplinary"],"day":"18","article_processing_charge":"No","status":"public","title":"Entangling microwaves with light","intvolume":" 380","_id":"13106","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification."}],"issue":"6646"},{"date_created":"2023-06-11T22:00:40Z","date_updated":"2023-08-02T06:12:39Z","author":[{"full_name":"Clozeau, Nicolas","last_name":"Clozeau","first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b"},{"full_name":"Josien, Marc","first_name":"Marc","last_name":"Josien"},{"full_name":"Otto, Felix","last_name":"Otto","first_name":"Felix"},{"last_name":"Xu","first_name":"Qiang","full_name":"Xu, Qiang"}],"publication_status":"epub_ahead","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","month":"05","publication_identifier":{"issn":["1615-3375"],"eissn":["1615-3383"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10208-023-09613-y","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000999623100001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10208-023-09613-y"}],"abstract":[{"text":"We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","status":"public","ddc":["510"],"_id":"13129","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"30","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-05-30T00:00:00Z","article_type":"original","publication":"Foundations of Computational Mathematics","citation":{"chicago":"Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.","mla":"Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023).","ista":"Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics.","ieee":"N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” Foundations of Computational Mathematics. Springer Nature, 2023.","apa":"Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y","ama":"Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y"}},{"ddc":["530"],"title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","department":[{"_id":"JoFi"}],"publisher":"Zenodo","year":"2023","_id":"13124","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-02T06:10:25Z","date_created":"2023-06-06T07:36:50Z","oa_version":"Published Version","author":[{"full_name":"Redchenko, Elena","first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander"},{"first_name":"Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya"},{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin"},{"full_name":"Poddubny, Alexander","first_name":"Alexander","last_name":"Poddubny"},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13117"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"mla":"Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567.","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7858567","open_access":"1"}],"doi":"10.5281/ZENODO.7858567","date_published":"2023-04-28T00:00:00Z","month":"04","day":"28","article_processing_charge":"No"},{"publisher":"Zenodo","department":[{"_id":"JoFi"}],"status":"public","title":"Entangling microwaves with light","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13122","year":"2023","oa_version":"Published Version","date_updated":"2023-08-02T06:08:56Z","date_created":"2023-06-06T06:46:16Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13106"}]},"author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","first_name":"Rishabh","last_name":"Sahu"}],"type":"research_data_reference","abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7789418"}],"citation":{"chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.","mla":"Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417.","short":"R. Sahu, (2023).","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417.","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417"},"doi":"10.5281/ZENODO.7789417","date_published":"2023-03-31T00:00:00Z","article_processing_charge":"No","day":"31","month":"03"},{"month":"06","publication_identifier":{"eissn":["2045-2322"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-023-35979-8","isi":1,"quality_controlled":"1","external_id":{"isi":["001006690200045"],"pmid":["37296138"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2023-06-26T09:58:53Z","article_number":"9382","date_updated":"2023-08-02T06:17:18Z","date_created":"2023-06-25T22:00:46Z","volume":13,"author":[{"last_name":"Vetrova","first_name":"Alexandra A.","full_name":"Vetrova, Alexandra A."},{"first_name":"Daria M.","last_name":"Kupaeva","full_name":"Kupaeva, Daria M."},{"last_name":"Kizenko","first_name":"Alena","id":"a521c60b-0815-11ed-9b02-b8bd522477c8","full_name":"Kizenko, Alena"},{"full_name":"Lebedeva, Tatiana S.","last_name":"Lebedeva","first_name":"Tatiana S."},{"last_name":"Walentek","first_name":"Peter","full_name":"Walentek, Peter"},{"last_name":"Tsikolia","first_name":"Nikoloz","full_name":"Tsikolia, Nikoloz"},{"full_name":"Kremnyov, Stanislav V.","last_name":"Kremnyov","first_name":"Stanislav V."}],"publication_status":"published","department":[{"_id":"GradSch"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","pmid":1,"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-06-09T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"ieee":"A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023.","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8","ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382.","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8."},"abstract":[{"lang":"eng","text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_ScientificReports_Vetrova.pdf","creator":"dernst","file_size":4844149,"content_type":"application/pdf","file_id":"13170","relation":"main_file","success":1,"checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","date_created":"2023-06-26T09:58:53Z","date_updated":"2023-06-26T09:58:53Z"}],"status":"public","ddc":["570"],"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","intvolume":" 13","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13166"},{"article_number":"184312","author":[{"first_name":"Pavel","last_name":"Orlov","full_name":"Orlov, Pavel"},{"full_name":"Tiutiakina, Anastasiia","first_name":"Anastasiia","last_name":"Tiutiakina"},{"last_name":"Sharipov","first_name":"Rustem","full_name":"Sharipov, Rustem"},{"first_name":"Elena","last_name":"Petrova","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","full_name":"Petrova, Elena"},{"full_name":"Gritsev, Vladimir","last_name":"Gritsev","first_name":"Vladimir"},{"last_name":"Kurlov","first_name":"Denis V.","full_name":"Kurlov, Denis V."}],"volume":107,"date_created":"2023-06-18T22:00:46Z","date_updated":"2023-08-02T06:16:02Z","acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","year":"2023","publisher":"American Physical Society","department":[{"_id":"GradSch"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"05","doi":"10.1103/PhysRevB.107.184312","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2303.00729"],"isi":["001003686900004"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.00729"}],"quality_controlled":"1","isi":1,"issue":"18","abstract":[{"text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"13138","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 107","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","citation":{"chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312.","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023.","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312"},"publication":"Physical Review B","article_type":"original"},{"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","acknowledgement":"We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.","year":"2023","pmid":1,"date_updated":"2023-08-02T06:27:55Z","date_created":"2023-07-12T07:32:58Z","volume":192,"author":[{"last_name":"Chen","first_name":"C","full_name":"Chen, C"},{"full_name":"Zhang, Y","last_name":"Zhang","first_name":"Y"},{"last_name":"Cai","first_name":"J","full_name":"Cai, J"},{"last_name":"Qiu","first_name":"Y","full_name":"Qiu, Y"},{"first_name":"L","last_name":"Li","full_name":"Li, L"},{"full_name":"Gao, C","first_name":"C","last_name":"Gao"},{"last_name":"Gao","first_name":"Y","full_name":"Gao, Y"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"last_name":"Wu","first_name":"S","full_name":"Wu, S"},{"full_name":"Wei, C","last_name":"Wei","first_name":"C"},{"full_name":"Chen, J","first_name":"J","last_name":"Chen"},{"last_name":"Xu","first_name":"T","full_name":"Xu, T"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Wang, J","first_name":"J","last_name":"Wang"},{"first_name":"R","last_name":"Li","full_name":"Li, R"},{"full_name":"Chao, D","last_name":"Chao","first_name":"D"},{"first_name":"B","last_name":"Zhang","full_name":"Zhang, B"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"},{"full_name":"Gao, Z","last_name":"Gao","first_name":"Z"}],"file_date_updated":"2023-07-13T13:26:33Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000971795800001"],"pmid":["37010107"]},"language":[{"iso":"eng"}],"doi":"10.1093/plphys/kiad207","month":"07","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"status":"public","ddc":["575"],"title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","intvolume":" 192","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13213","oa_version":"Published Version","file":[{"file_size":2076977,"content_type":"application/pdf","creator":"cchlebak","file_name":"2023_PlantPhys_Chen.pdf","access_level":"open_access","date_updated":"2023-07-13T13:26:33Z","date_created":"2023-07-13T13:26:33Z","checksum":"5492e1d18ac3eaf202633d210fa0fb75","success":1,"relation":"main_file","file_id":"13220"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth."}],"issue":"3","article_type":"original","page":"2243-2260","publication":"Plant Physiology","citation":{"chicago":"Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207.","mla":"Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207.","short":"C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260.","ista":"Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260.","apa":"Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207","ieee":"C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.","ama":"Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207"},"date_published":"2023-07-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"publisher":"Frontiers","department":[{"_id":"CaGu"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.","volume":14,"date_updated":"2023-08-02T06:25:04Z","date_created":"2023-02-02T08:13:28Z","author":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"full_name":"Bruneaux, L","last_name":"Bruneaux","first_name":"L"},{"last_name":"Oikonomou","first_name":"P","full_name":"Oikonomou, P"},{"last_name":"Aldana","first_name":"M","full_name":"Aldana, M"},{"full_name":"Cluzel, P","first_name":"P","last_name":"Cluzel"}],"article_number":"1049255","file_date_updated":"2023-07-31T07:16:34Z","quality_controlled":"1","isi":1,"external_id":{"pmid":["37485524"],"isi":["001030002600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1049255","publication_identifier":{"eissn":["1664-302X"]},"month":"06","intvolume":" 14","ddc":["570"],"status":"public","title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12478","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":6452841,"file_name":"2023_FrontiersMicrobiology_Guet.pdf","access_level":"open_access","date_updated":"2023-07-31T07:16:34Z","date_created":"2023-07-31T07:16:34Z","success":1,"checksum":"7dd322347512afaa5daf72a0154f2f07","file_id":"13322","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype."}],"article_type":"original","citation":{"ama":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1049255","ista":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 14, 1049255.","ieee":"C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","apa":"Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., & Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1049255","mla":"Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology, vol. 14, 1049255, Frontiers, 2023, doi:10.3389/fmicb.2023.1049255.","short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","chicago":"Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1049255."},"publication":"Frontiers in Microbiology","date_published":"2023-06-20T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"20"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13237","status":"public","title":"Amyloid formation as a protein phase transition","intvolume":" 5","oa_version":"None","type":"journal_article","abstract":[{"text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.","lang":"eng"}],"publication":"Nature Reviews Physics","citation":{"mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9.","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9.","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397. doi:10.1038/s42254-023-00598-9","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 379–397, 2023.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., & Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9"},"article_type":"original","page":"379–397","date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2023","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"Springer Nature","author":[{"first_name":"Thomas C.T.","last_name":"Michaels","full_name":"Michaels, Thomas C.T."},{"full_name":"Qian, Daoyuan","first_name":"Daoyuan","last_name":"Qian"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Vendruscolo, Michele","first_name":"Michele","last_name":"Vendruscolo"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."}],"date_updated":"2023-08-02T06:28:38Z","date_created":"2023-07-16T22:01:12Z","volume":5,"external_id":{"isi":["001017539800001"]},"quality_controlled":"1","isi":1,"doi":"10.1038/s42254-023-00598-9","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["2522-5820"]}},{"day":"08","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-06-08T00:00:00Z","publication":"PLoS Biology","citation":{"chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:10.1371/journal.pbio.3002146.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146","ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146. doi:10.1371/journal.pbio.3002146"},"article_type":"original","page":"e3002146","abstract":[{"lang":"eng","text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"file_size":4431723,"content_type":"application/pdf","creator":"dernst","file_name":"2023_PloSBiology_Shamipour.pdf","access_level":"open_access","date_updated":"2023-07-18T07:59:58Z","date_created":"2023-07-18T07:59:58Z","checksum":"8e88cb0e5a6433a2f1939a9030bed384","success":1,"relation":"main_file","file_id":"13246"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13229","ddc":["570"],"title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","status":"public","intvolume":" 21","month":"06","publication_identifier":{"eissn":["1545-7885"]},"doi":"10.1371/journal.pbio.3002146","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37289834"],"isi":["001003199100005"]},"quality_controlled":"1","isi":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"file_date_updated":"2023-07-18T07:59:58Z","ec_funded":1,"author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"full_name":"Hofmann, Laura","first_name":"Laura","last_name":"Hofmann","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031"},{"full_name":"Steccari, Irene","first_name":"Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"date_updated":"2023-08-02T06:33:14Z","date_created":"2023-07-16T22:01:09Z","volume":21,"year":"2023","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Public Library of Science"},{"abstract":[{"text":"Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"Mosaic_asymmetries.pdf","access_level":"open_access","creator":"ggrosjea","file_size":1127040,"content_type":"application/pdf","file_id":"13198","relation":"main_file","date_updated":"2023-07-07T12:49:51Z","date_created":"2023-07-07T12:49:51Z","success":1,"checksum":"75584730d9cdd50eeccb4c52c509776d"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13197","ddc":["537"],"status":"public","title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","intvolume":" 7","day":"13","article_processing_charge":"No","has_accepted_license":"1","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"],"date_published":"2023-06-13T00:00:00Z","publication":"Physical Review Materials","citation":{"ama":"Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601","ista":"Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601.","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:10.1103/physrevmaterials.7.065601.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials. American Physical Society, 2023. https://doi.org/10.1103/physrevmaterials.7.065601."},"article_type":"original","file_date_updated":"2023-07-07T12:49:51Z","ec_funded":1,"article_number":"065601","author":[{"full_name":"Grosjean, Galien M","last_name":"Grosjean","first_name":"Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425"},{"full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-02T06:34:47Z","date_created":"2023-07-07T12:48:01Z","volume":7,"year":"2023","acknowledgement":"This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. ","publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","month":"06","publication_identifier":{"issn":["2475-9953"]},"doi":"10.1103/physrevmaterials.7.065601","language":[{"iso":"eng"}],"external_id":{"arxiv":["2304.12861"],"isi":["001019565900002"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}]},{"type":"journal_article","abstract":[{"text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.","lang":"eng"}],"issue":"6","title":"Environmental dynamics shape perceptual decision bias","ddc":["570"],"status":"public","intvolume":" 19","_id":"13230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":2281868,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_PloSCompBio_Charlton.pdf","checksum":"800761fa2c647fabd6ad034589bc526e","success":1,"date_created":"2023-07-18T08:07:59Z","date_updated":"2023-07-18T08:07:59Z","relation":"main_file","file_id":"13247"}],"scopus_import":"1","day":"08","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"PLoS Computational Biology","citation":{"mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1011104.","short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6). doi:10.1371/journal.pcbi.1011104","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational Biology, vol. 19, no. 6. Public Library of Science, 2023.","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104"},"date_published":"2023-06-08T00:00:00Z","article_number":"e1011104","file_date_updated":"2023-07-18T08:07:59Z","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"MaJö"}],"year":"2023","acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","pmid":1,"date_created":"2023-07-16T22:01:09Z","date_updated":"2023-08-02T06:33:50Z","volume":19,"author":[{"last_name":"Charlton","first_name":"Julie A.","full_name":"Charlton, Julie A."},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F"},{"last_name":"Bai","first_name":"Yoon H.","full_name":"Bai, Yoon H."},{"full_name":"Hermundstad, Ann M.","first_name":"Ann M.","last_name":"Hermundstad"},{"first_name":"Robbe L.T.","last_name":"Goris","full_name":"Goris, Robbe L.T."}],"month":"06","publication_identifier":{"eissn":["1553-7358"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001003410200003"],"pmid":["37289753"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1011104"},{"file_date_updated":"2023-07-18T07:25:43Z","article_number":"1014","author":[{"full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin","first_name":"Dmitri"},{"first_name":"Mikalai","last_name":"Katsin","full_name":"Katsin, Mikalai"},{"last_name":"Stegantseva","first_name":"Maria","full_name":"Stegantseva, Maria"},{"first_name":"Sergey","last_name":"Golenchenko","full_name":"Golenchenko, Sergey"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"full_name":"Dubovik, Simon","first_name":"Simon","last_name":"Dubovik"},{"first_name":"Dzmitry","last_name":"Lutskovich","full_name":"Lutskovich, Dzmitry"},{"last_name":"Kavaleuski","first_name":"Anton","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton"},{"first_name":"Alexander","last_name":"Meleshko","full_name":"Meleshko, Alexander"}],"date_created":"2023-07-16T22:01:10Z","date_updated":"2023-08-02T06:31:19Z","volume":11,"year":"2023","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","publication_status":"published","publisher":"MDPI","department":[{"_id":"LeSa"}],"month":"06","publication_identifier":{"eissn":["2076-393X"]},"doi":"10.3390/vaccines11061014","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001017740000001"]},"quality_controlled":"1","isi":1,"abstract":[{"text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.","lang":"eng"}],"issue":"6","type":"journal_article","file":[{"relation":"main_file","file_id":"13244","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","success":1,"date_created":"2023-07-18T07:25:43Z","date_updated":"2023-07-18T07:25:43Z","access_level":"open_access","file_name":"2023_Vaccines_Dormeshkin.pdf","content_type":"application/pdf","file_size":2339746,"creator":"dernst"}],"oa_version":"Published Version","_id":"13232","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","intvolume":" 11","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-06-01T00:00:00Z","publication":"Vaccines","citation":{"chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","ieee":"D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014"},"article_type":"original"},{"oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13235","intvolume":" 17","status":"public","title":"Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance","issue":"12","abstract":[{"text":"AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications.","lang":"eng"}],"type":"journal_article","date_published":"2023-06-13T00:00:00Z","citation":{"chicago":"Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c03541.","short":"Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934.","mla":"Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:10.1021/acsnano.3c03541.","apa":"Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c03541","ieee":"Y. Liu et al., “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” ACS Nano, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.","ista":"Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934.","ama":"Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 2023;17(12):11923–11934. doi:10.1021/acsnano.3c03541"},"publication":"ACS Nano","page":"11923–11934","article_type":"original","article_processing_charge":"No","day":"13","scopus_import":"1","author":[{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"full_name":"Li, Mingquan","first_name":"Mingquan","last_name":"Li"},{"last_name":"Wan","first_name":"Shanhong","full_name":"Wan, Shanhong"},{"full_name":"Lim, Khak Ho","first_name":"Khak Ho","last_name":"Lim"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Hong, Min","last_name":"Hong","first_name":"Min"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"volume":17,"date_created":"2023-07-16T22:01:11Z","date_updated":"2023-08-02T06:29:55Z","pmid":1,"acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","year":"2023","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"publication_status":"published","doi":"10.1021/acsnano.3c03541","language":[{"iso":"eng"}],"external_id":{"pmid":["37310395"],"isi":["001008564800001"]},"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"month":"06"},{"article_number":"065207","department":[{"_id":"BiCh"}],"publisher":"American Physical Society","publication_status":"published","year":"2023","acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","volume":107,"date_created":"2023-07-16T22:01:10Z","date_updated":"2023-08-02T06:30:46Z","author":[{"last_name":"Schörner","first_name":"Maximilian","full_name":"Schörner, Maximilian"},{"full_name":"Bethkenhagen, Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy","last_name":"Bethkenhagen"},{"first_name":"Tilo","last_name":"Döppner","full_name":"Döppner, Tilo"},{"full_name":"Kraus, Dominik","last_name":"Kraus","first_name":"Dominik"},{"full_name":"Fletcher, Luke B.","last_name":"Fletcher","first_name":"Luke B."},{"last_name":"Glenzer","first_name":"Siegfried H.","full_name":"Glenzer, Siegfried H."},{"first_name":"Ronald","last_name":"Redmer","full_name":"Redmer, Ronald"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"month":"06","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01545","open_access":"1"}],"external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.107.065207","type":"journal_article","issue":"6","abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"intvolume":" 107","status":"public","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13231","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"14","article_type":"original","citation":{"mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","ieee":"M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, vol. 107, no. 6. American Physical Society, 2023.","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207"},"publication":"Physical Review E","date_published":"2023-06-14T00:00:00Z"},{"publication_status":"published","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"publisher":"American Physical Society","year":"2023","acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","date_created":"2023-07-16T22:01:10Z","date_updated":"2023-08-02T06:31:52Z","volume":107,"author":[{"last_name":"Agafonova","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","full_name":"Agafonova, Sofya"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"article_number":"L061304","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["001019748000005"],"arxiv":["2302.01022"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.01022"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.L061304","month":"06","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"title":"Finite-range bias in fitting three-body loss to the zero-range model","status":"public","intvolume":" 107","_id":"13233","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.","lang":"eng"}],"issue":"6","article_type":"letter_note","publication":"Physical Review A","citation":{"mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","apa":"Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304"},"date_published":"2023-06-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No"},{"external_id":{"isi":["001024920300002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41612-023-00411-5","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["2397-3722"]},"year":"2023","acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","author":[{"last_name":"Goswami","first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"Goswami, Bidyut B"},{"last_name":"An","first_name":"Soon Il","full_name":"An, Soon Il"}],"date_updated":"2023-08-02T06:38:07Z","date_created":"2023-07-23T22:01:10Z","volume":6,"article_number":"82","file_date_updated":"2023-07-31T08:00:01Z","publication":"npj Climate and Atmospheric Science","citation":{"chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.","apa":"GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023.","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5"},"article_type":"original","date_published":"2023-07-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"Yes","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13256","ddc":["550"],"status":"public","title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","intvolume":" 6","file":[{"date_updated":"2023-07-31T08:00:01Z","date_created":"2023-07-31T08:00:01Z","checksum":"e9967d436a83b8ffcc6f58782e1f7500","success":1,"relation":"main_file","file_id":"13326","file_size":1750712,"content_type":"application/pdf","creator":"dernst","file_name":"2023_npjclimate_Goswami.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate."}]},{"month":"07","publication_identifier":{"eissn":["1759-6653"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001023444700003"],"pmid":["37341535"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1093/gbe/evad113","language":[{"iso":"eng"}],"article_number":"evad113","file_date_updated":"2023-08-01T06:58:34Z","year":"2023","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","pmid":1,"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"BeVi"}],"author":[{"full_name":"De Castro Barbosa Rodrigues Barata, Carolina","first_name":"Carolina","last_name":"De Castro Barbosa Rodrigues Barata","id":"20565186-803f-11ed-ab7e-96a4ff7694ef"},{"first_name":"Rhonda R.","last_name":"Snook","full_name":"Snook, Rhonda R."},{"full_name":"Ritchie, Michael G.","first_name":"Michael G.","last_name":"Ritchie"},{"full_name":"Kosiol, Carolin","last_name":"Kosiol","first_name":"Carolin"}],"related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"date_created":"2023-07-23T22:01:11Z","date_updated":"2023-08-02T06:42:35Z","volume":15,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Genome biology and evolution","citation":{"mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023."},"article_type":"original","date_published":"2023-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13260","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","status":"public","ddc":["570"],"intvolume":" 15","file":[{"relation":"main_file","file_id":"13339","checksum":"70de3c4878de6efe00dc56de2df8812f","success":1,"date_created":"2023-08-01T06:58:34Z","date_updated":"2023-08-01T06:58:34Z","access_level":"open_access","file_name":"2023_GBE_Barata.pdf","content_type":"application/pdf","file_size":2382587,"creator":"dernst"}],"oa_version":"Published Version"},{"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13346","status":"public","title":"Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices","intvolume":" 17","abstract":[{"lang":"eng","text":"The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities."}],"issue":"1","type":"journal_article","date_published":"2023-01-10T00:00:00Z","publication":"ACS Nano","citation":{"ama":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 2023;17(1):275-287. doi:10.1021/acsnano.2c07558","ista":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. 2023. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 17(1), 275–287.","ieee":"C. Lionello, C. Perego, A. Gardin, R. Klajn, and G. M. Pavan, “Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices,” ACS Nano, vol. 17, no. 1. American Chemical Society, pp. 275–287, 2023.","apa":"Lionello, C., Perego, C., Gardin, A., Klajn, R., & Pavan, G. M. (2023). Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.2c07558","mla":"Lionello, Chiara, et al. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano, vol. 17, no. 1, American Chemical Society, 2023, pp. 275–87, doi:10.1021/acsnano.2c07558.","short":"C. Lionello, C. Perego, A. Gardin, R. Klajn, G.M. Pavan, ACS Nano 17 (2023) 275–287.","chicago":"Lionello, Chiara, Claudio Perego, Andrea Gardin, Rafal Klajn, and Giovanni M. Pavan. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.2c07558."},"article_type":"original","page":"275-287","day":"10","article_processing_charge":"No","scopus_import":"1","keyword":["General Physics and Astronomy","General Engineering","General Materials Science"],"author":[{"first_name":"Chiara","last_name":"Lionello","full_name":"Lionello, Chiara"},{"last_name":"Perego","first_name":"Claudio","full_name":"Perego, Claudio"},{"full_name":"Gardin, Andrea","first_name":"Andrea","last_name":"Gardin"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"},{"last_name":"Pavan","first_name":"Giovanni M.","full_name":"Pavan, Giovanni M."}],"date_updated":"2023-08-02T06:51:15Z","date_created":"2023-08-01T09:30:29Z","volume":17,"year":"2023","publication_status":"published","publisher":"American Chemical Society","extern":"1","doi":"10.1021/acsnano.2c07558","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.2c07558"}],"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]}},{"article_processing_charge":"No","day":"06","month":"07","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2307.03237","open_access":"1"}],"citation":{"short":"D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).","mla":"Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.","chicago":"Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237.","ama":"Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237","apa":"Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237","ieee":"D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. .","ista":"Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237."},"external_id":{"arxiv":["2307.03237"]},"oa":1,"publication":"arXiv","doi":"10.48550/arXiv.2307.03237","date_published":"2023-07-06T00:00:00Z","language":[{"iso":"eng"}],"type":"preprint","article_number":"2307.03237","abstract":[{"lang":"eng","text":"Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing."}],"year":"2023","_id":"13447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LiBu"}],"publication_status":"submitted","title":"Asteroseismology with the Roman galactic bulge time-domain survey","status":"public","author":[{"first_name":"Daniel","last_name":"Huber","full_name":"Huber, Daniel"},{"full_name":"Pinsonneault, Marc","first_name":"Marc","last_name":"Pinsonneault"},{"full_name":"Beck, Paul","first_name":"Paul","last_name":"Beck"},{"last_name":"Bedding","first_name":"Timothy R.","full_name":"Bedding, Timothy R."},{"full_name":"Joss Bland-Hawthorn, Joss Bland-Hawthorn","last_name":"Joss Bland-Hawthorn","first_name":"Joss Bland-Hawthorn"},{"first_name":"Sylvain N.","last_name":"Breton","full_name":"Breton, Sylvain N."},{"id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","first_name":"Lisa Annabelle","last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle"},{"first_name":"William J.","last_name":"Chaplin","full_name":"Chaplin, William J."},{"last_name":"Garcia","first_name":"Rafael A.","full_name":"Garcia, Rafael A."},{"last_name":"Grunblatt","first_name":"Samuel K.","full_name":"Grunblatt, Samuel K."},{"full_name":"Guzik, Joyce A.","last_name":"Guzik","first_name":"Joyce A."},{"last_name":"Hekker","first_name":"Saskia","full_name":"Hekker, Saskia"},{"first_name":"Steven D.","last_name":"Kawaler","full_name":"Kawaler, Steven D."},{"first_name":"Stephane","last_name":"Mathis","full_name":"Mathis, Stephane"},{"full_name":"Mathur, Savita","last_name":"Mathur","first_name":"Savita"},{"full_name":"Metcalfe, Travis","last_name":"Metcalfe","first_name":"Travis"},{"full_name":"Mosser, Benoit","last_name":"Mosser","first_name":"Benoit"},{"last_name":"Ness","first_name":"Melissa K.","full_name":"Ness, Melissa K."},{"last_name":"Piro","first_name":"Anthony L.","full_name":"Piro, Anthony L."},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"full_name":"Sharma, Sanjib","first_name":"Sanjib","last_name":"Sharma"},{"last_name":"Soderblom","first_name":"David R.","full_name":"Soderblom, David R."},{"last_name":"Stassun","first_name":"Keivan G.","full_name":"Stassun, Keivan G."},{"first_name":"Dennis","last_name":"Stello","full_name":"Stello, Dennis"},{"full_name":"Tayar, Jamie","first_name":"Jamie","last_name":"Tayar"},{"last_name":"Belle","first_name":"Gerard T. van","full_name":"Belle, Gerard T. van"},{"first_name":"Joel C.","last_name":"Zinn","full_name":"Zinn, Joel C."}],"oa_version":"Preprint","date_created":"2023-08-02T07:30:43Z","date_updated":"2023-08-02T07:36:00Z"},{"month":"02","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"quality_controlled":"1","external_id":{"pmid":["36757850"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c11973"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/jacs.2c11973","extern":"1","publication_status":"published","publisher":"American Chemical Society","year":"2023","pmid":1,"date_updated":"2023-08-02T10:44:22Z","date_created":"2023-08-01T09:33:08Z","volume":145,"author":[{"full_name":"Wang, Jinhua","first_name":"Jinhua","last_name":"Wang"},{"first_name":"Tzuf Shay","last_name":"Peled","full_name":"Peled, Tzuf Shay"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"scopus_import":"1","day":"09","article_processing_charge":"No","article_type":"original","page":"4098-4108","publication":"Journal of the American Chemical Society","citation":{"mla":"Wang, Jinhua, et al. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American Chemical Society, vol. 145, no. 7, American Chemical Society, 2023, pp. 4098–108, doi:10.1021/jacs.2c11973.","short":"J. Wang, T.S. Peled, R. Klajn, Journal of the American Chemical Society 145 (2023) 4098–4108.","chicago":"Wang, Jinhua, Tzuf Shay Peled, and Rafal Klajn. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.2c11973.","ama":"Wang J, Peled TS, Klajn R. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 2023;145(7):4098-4108. doi:10.1021/jacs.2c11973","ista":"Wang J, Peled TS, Klajn R. 2023. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 145(7), 4098–4108.","ieee":"J. Wang, T. S. Peled, and R. Klajn, “Photocleavable anionic glues for light-responsive nanoparticle aggregates,” Journal of the American Chemical Society, vol. 145, no. 7. American Chemical Society, pp. 4098–4108, 2023.","apa":"Wang, J., Peled, T. S., & Klajn, R. (2023). Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.2c11973"},"date_published":"2023-02-09T00:00:00Z","type":"journal_article","abstract":[{"text":"Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus.","lang":"eng"}],"issue":"7","title":"Photocleavable anionic glues for light-responsive nanoparticle aggregates","status":"public","intvolume":" 145","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13354","oa_version":"Published Version"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"_id":"12781","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["570","572"],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","oa_version":"Published Version","file":[{"file_id":"12852","embargo":"2024-04-20","relation":"main_file","checksum":"5ebb6345cb4119f93460c81310265a6d","date_created":"2023-04-19T14:33:41Z","date_updated":"2023-04-19T14:33:41Z","access_level":"closed","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","embargo_to":"local","creator":"vkravchu","file_size":6071553,"content_type":"application/pdf"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19468766,"creator":"vkravchu","embargo_to":"local","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","access_level":"closed","date_updated":"2023-04-20T07:02:59Z","date_created":"2023-04-19T14:33:52Z","checksum":"c12055c48411d030d2afa51de2166221","relation":"source_file","embargo":"2024-04-20","file_id":"12853"}],"has_accepted_license":"1","article_processing_charge":"No","day":"23","citation":{"short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria."},"page":"127","date_published":"2023-03-23T00:00:00Z","ec_funded":1,"file_date_updated":"2023-04-20T07:02:59Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-04T08:54:51Z","date_created":"2023-03-31T12:24:42Z","publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"month":"03","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"grant_number":"101020697","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines"}],"doi":"10.15479/at:ista:12781","language":[{"iso":"eng"}],"supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"degree_awarded":"PhD"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"13074","title":"Efficiency and generalization of sparse neural networks","status":"public","ddc":["000"],"file":[{"content_type":"application/pdf","file_size":2152072,"creator":"epeste","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","access_level":"open_access","date_updated":"2023-05-24T16:11:16Z","date_created":"2023-05-24T16:11:16Z","checksum":"6b3354968403cb9d48cc5a83611fb571","success":1,"relation":"main_file","file_id":"13087"},{"date_created":"2023-05-24T16:12:59Z","date_updated":"2023-05-24T16:12:59Z","checksum":"8d0df94bbcf4db72c991f22503b3fd60","file_id":"13088","relation":"source_file","creator":"epeste","content_type":"application/zip","file_size":1658293,"file_name":"PhD_Thesis_APeste.zip","access_level":"closed"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"citation":{"ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074."},"page":"147","date_published":"2023-05-23T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"23","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"published","related_material":{"record":[{"id":"11458","status":"public","relation":"part_of_dissertation"},{"id":"13053","status":"public","relation":"part_of_dissertation"},{"id":"12299","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-23T17:07:53Z","date_updated":"2023-08-04T10:33:27Z","ec_funded":1,"file_date_updated":"2023-05-24T16:12:59Z","oa":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"doi":"10.15479/at:ista:13074","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663-337X"]},"month":"05"},{"publication_identifier":{"isbn":["978-3-99078-032-9"],"issn":["2663-337X"]},"month":"05","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.15479/at:ista:12964","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"}],"degree_awarded":"PhD","ec_funded":1,"file_date_updated":"2023-05-19T07:04:25Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8602"}]},"author":[{"full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock","first_name":"Daniel R"}],"date_updated":"2023-08-04T11:02:40Z","date_created":"2023-05-15T14:52:36Z","has_accepted_license":"1","article_processing_charge":"No","day":"17","citation":{"ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964."},"page":"146","date_published":"2023-05-17T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12964","ddc":["530"],"status":"public","title":"Mechanochemical pattern formation across biological scales","file":[{"creator":"dboocock","content_type":"application/pdf","file_size":40414730,"access_level":"closed","file_name":"thesis_boocock.pdf","embargo_to":"open_access","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","date_updated":"2023-05-19T07:04:25Z","date_created":"2023-05-17T13:39:54Z","embargo":"2024-05-17","file_id":"12988","relation":"main_file"},{"file_name":"thesis_boocock.zip","access_level":"closed","creator":"dboocock","file_size":34338567,"content_type":"application/zip","file_id":"12989","relation":"source_file","date_created":"2023-05-17T13:39:53Z","date_updated":"2023-05-17T14:35:13Z","checksum":"581a2313ffeb40fe77e8a122a25a7795"}],"oa_version":"Published Version"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","article_type":"original","citation":{"apa":"Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201","ieee":"P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization proximity effect in a two-species bosonic Hubbard model,” Physical Review B, vol. 108, no. 5. American Physical Society, 2023.","ista":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201.","ama":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5). doi:10.1103/physrevb.108.054201","chicago":"Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201.","short":"P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).","mla":"Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American Physical Society, 2023, doi:10.1103/physrevb.108.054201."},"publication":"Physical Review B","date_published":"2023-08-01T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons.","lang":"eng"}],"intvolume":" 108","ddc":["530"],"status":"public","title":"Many-body localization proximity effect in a two-species bosonic Hubbard model","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13963","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_PhysRevB_Brighi.pdf","content_type":"application/pdf","file_size":3051398,"creator":"dernst","relation":"main_file","file_id":"13981","checksum":"f763000339b5fd543c14377109920690","success":1,"date_created":"2023-08-07T09:48:08Z","date_updated":"2023-08-07T09:48:08Z"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"08","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2303.16876"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.108.054201","article_number":"054201","ec_funded":1,"file_date_updated":"2023-08-07T09:48:08Z","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"We thank A. A. Michailidis and A. Mirlin for insightful discussions. P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [60].","year":"2023","volume":108,"date_updated":"2023-08-07T09:51:39Z","date_created":"2023-08-05T18:25:22Z","author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ljubotina, Marko","last_name":"Ljubotina","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}]},{"_id":"13966","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling","intvolume":" 108","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams."}],"issue":"4","publication":"Physical Review B","citation":{"ama":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115","ista":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 108(4), 045115.","ieee":"G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling,” Physical Review B, vol. 108, no. 4. American Physical Society, 2023.","apa":"Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.045115","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.","short":"G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).","chicago":"Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.045115."},"article_type":"original","date_published":"2023-07-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","year":"2023","acknowledgement":"We acknowledge stimulating discussions with Sergey Varganov, Artur Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov, Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L. acknowledges support by the FWF under Project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). The authors acknowledge support by the state of Baden-Württemberg through bwHPC.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"},{"_id":"TaHa"}],"author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo"},{"full_name":"Ho, Quoc P","last_name":"Ho","first_name":"Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"last_name":"Tscherbul","first_name":"T. V.","full_name":"Tscherbul, T. V."}],"date_created":"2023-08-06T22:01:10Z","date_updated":"2023-08-07T08:41:29Z","volume":108,"article_number":"045115","ec_funded":1,"external_id":{"arxiv":["2203.12666"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.12666","open_access":"1"}],"quality_controlled":"1","project":[{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"grant_number":"M02751","_id":"26B96266-B435-11E9-9278-68D0E5697425","name":"Algebro-Geometric Applications of Factorization Homology","call_identifier":"FWF"},{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevB.108.045115","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"month":"07","publication_identifier":{"issn":["0078-6209"],"eissn":["2333-3553"]},"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.15227/orgsyn.100.0271","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.15227/orgsyn.100.0271","publication_status":"published","department":[{"_id":"BaPi"}],"publisher":"Organic Syntheses","year":"2023","date_updated":"2023-08-07T08:21:45Z","date_created":"2023-08-06T22:01:11Z","volume":100,"author":[{"full_name":"Madani, Amiera","first_name":"Amiera","last_name":"Madani"},{"full_name":"Sletten, Eric T.","first_name":"Eric T.","last_name":"Sletten"},{"last_name":"Cavedon","first_name":"Cristian","full_name":"Cavedon, Cristian"},{"first_name":"Peter H.","last_name":"Seeberger","full_name":"Seeberger, Peter H."},{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"}],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"271-286","publication":"Organic Syntheses","citation":{"mla":"Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.","short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286.","chicago":"Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.","ama":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271","ista":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286.","ieee":"A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.","apa":"Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271"},"date_published":"2023-07-01T00:00:00Z","type":"journal_article","title":"Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose","status":"public","intvolume":" 100","_id":"13970","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"03","citation":{"chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y"},"publication":"Nature Communications","article_type":"original","date_published":"2023-06-03T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense."}],"_id":"13127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 14","status":"public","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","ddc":["570"],"file":[{"creator":"dernst","file_size":2358167,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_NatureComm_CasillasPerez.pdf","success":1,"checksum":"4af0393e3ed47b3fc46e68b81c3c1007","date_created":"2023-06-13T08:05:46Z","date_updated":"2023-06-13T08:05:46Z","file_id":"13132","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37270641"],"isi":["001002562700005"]},"project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-023-38947-y","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"article_number":"3232","ec_funded":1,"file_date_updated":"2023-06-13T08:05:46Z","pmid":1,"acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","year":"2023","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"12945"}]},"author":[{"full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'Ová","first_name":"Katarína","full_name":"Bod'Ová, Katarína"},{"full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"volume":14,"date_updated":"2023-08-07T13:09:09Z","date_created":"2023-06-11T22:00:40Z"},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"citation":{"ama":"Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945","ieee":"S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.","apa":"Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12945","ista":"Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12945.","short":"S. Cremer, (2023).","mla":"Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12945.","chicago":"Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12945."},"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.15479/AT:ISTA:12945","date_published":"2023-05-12T00:00:00Z","keyword":["collective behavior","host-pathogen interactions","social immunity","epidemiology","social insects","probabilistic modeling"],"month":"05","day":"12","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"title":"Data from: \"Dynamic pathogen detection and social feedback shape collective hygiene in ants\" ","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SyCr"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","_id":"12945","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-07T13:09:09Z","date_created":"2023-05-11T21:35:17Z","oa_version":"None","file":[{"access_level":"open_access","file_name":"Experimental_data.zip","file_size":3414674,"content_type":"application/zip","creator":"scremer","relation":"main_file","file_id":"12947","checksum":"3eadf17fd59ad8c98bf10bf63061863c","success":1,"date_updated":"2023-05-12T08:04:04Z","date_created":"2023-05-12T08:04:04Z"},{"file_id":"12948","relation":"main_file","date_created":"2023-05-12T08:04:08Z","date_updated":"2023-05-12T08:04:08Z","success":1,"checksum":"1b5e8e01a0989154a76b44e6d8d68f89","file_name":"README_Experimental_Data.md","access_level":"open_access","creator":"scremer","content_type":"application/octet-stream","file_size":2113}],"author":[{"full_name":"Cremer, Sylvia","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13127"}]},"contributor":[{"last_name":"Casillas Perez","contributor_type":"data_collector","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","contributor_type":"data_collector","first_name":"Anna V"},{"first_name":"Katarina","contributor_type":"researcher","last_name":"Bodova"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","contributor_type":"supervisor","first_name":"Gašper"}],"type":"research_data","abstract":[{"lang":"eng","text":"basic data for use in code for experimental data analysis for manuscript under revision: \r\nDynamic pathogen detection and social feedback shape collective hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S"}],"file_date_updated":"2023-05-12T08:04:08Z"},{"ec_funded":1,"file_date_updated":"2023-05-02T07:43:18Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"10806","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"status":"public","relation":"part_of_dissertation","id":"12237"},{"id":"9118","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"10123"}]},"author":[{"first_name":"Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","full_name":"Calcabrini, Mariano"}],"date_updated":"2023-08-14T07:25:26Z","date_created":"2023-05-02T07:58:57Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"month":"04","oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"doi":"10.15479/at:ista:12885","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"supervisor":[{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12885","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","ddc":["546","541"],"status":"public","file":[{"file_id":"12887","relation":"source_file","checksum":"9347b0e09425f56fdcede5d3528404dc","date_updated":"2023-05-02T07:43:18Z","date_created":"2023-05-02T07:43:18Z","access_level":"closed","file_name":"Thesis_Calcabrini.docx","creator":"mcalcabr","file_size":99627036,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","file_id":"12888","date_updated":"2023-05-02T07:42:45Z","date_created":"2023-05-02T07:42:45Z","checksum":"2d188b76621086cd384f0b9264b0a576","success":1,"file_name":"Thesis_Calcabrini_pdfa.pdf","access_level":"open_access","content_type":"application/pdf","file_size":8742220,"creator":"mcalcabr"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"28","citation":{"short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria."},"page":"82","date_published":"2023-04-28T00:00:00Z"},{"month":"03","publication_identifier":{"issn":["1424-0637"]},"doi":"10.1007/s00023-022-01220-x","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000837499800002"],"arxiv":["2105.08303"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M03337","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"file_date_updated":"2023-08-14T11:38:28Z","ec_funded":1,"author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","last_name":"Zhang","full_name":"Zhang, Haonan"}],"date_created":"2022-09-11T22:01:57Z","date_updated":"2023-08-14T11:39:28Z","volume":24,"year":"2023","acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","publication":"Annales Henri Poincare","citation":{"ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 717–750, 2023.","apa":"Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750."},"article_type":"original","page":"717-750","abstract":[{"lang":"eng","text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14051","date_updated":"2023-08-14T11:38:28Z","date_created":"2023-08-14T11:38:28Z","checksum":"8c7b185eba5ccd92ef55c120f654222c","success":1,"file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","access_level":"open_access","file_size":554871,"content_type":"application/pdf","creator":"dernst"}],"_id":"12087","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"status":"public","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","intvolume":" 24"},{"publication_identifier":{"eissn":["1565-8511"]},"month":"03","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000904950300003"],"arxiv":["1903.05923"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11856-022-2448-6","file_date_updated":"2021-07-14T07:41:50Z","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","year":"2023","volume":253,"date_updated":"2023-08-14T11:26:34Z","date_created":"2021-07-14T07:01:28Z","author":[{"full_name":"Dymond, Michael","first_name":"Michael","last_name":"Dymond"},{"first_name":"Vojtech","last_name":"Kaluza","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","orcid":"0000-0002-2512-8698","full_name":"Kaluza, Vojtech"}],"keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"501-554","article_type":"original","citation":{"short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.","mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6.","ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6","apa":"Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.","ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554."},"publication":"Israel Journal of Mathematics","date_published":"2023-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities.","lang":"eng"}],"intvolume":" 253","ddc":["515","516"],"title":"Highly irregular separated nets","status":"public","_id":"9652","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_name":"separated_nets.pdf","access_level":"open_access","creator":"vkaluza","file_size":900422,"content_type":"application/pdf","file_id":"9653","relation":"main_file","date_created":"2021-07-14T07:41:50Z","date_updated":"2021-07-14T07:41:50Z","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1"}]},{"day":"15","article_processing_charge":"No","scopus_import":"1","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"date_published":"2023-03-15T00:00:00Z","publication":"Applied Surface Science","citation":{"chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science. Elsevier, 2023. https://doi.org/10.1016/j.apsusc.2022.156101.","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” Applied Surface Science, vol. 613, 156101, Elsevier, 2023, doi:10.1016/j.apsusc.2022.156101.","ieee":"L. Zhang et al., “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” Applied Surface Science, vol. 613. Elsevier, 2023.","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. Elsevier. https://doi.org/10.1016/j.apsusc.2022.156101","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 2023;613. doi:10.1016/j.apsusc.2022.156101"},"article_type":"original","abstract":[{"text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"12113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","status":"public","intvolume":" 613","month":"03","publication_identifier":{"issn":["0169-4332"]},"doi":"10.1016/j.apsusc.2022.156101","language":[{"iso":"eng"}],"external_id":{"isi":["000911497000001"]},"isi":1,"quality_controlled":"1","article_number":"156101","author":[{"last_name":"Zhang","first_name":"Li","full_name":"Zhang, Li"},{"full_name":"Liu, Xingyu","first_name":"Xingyu","last_name":"Liu"},{"full_name":"Wu, Ting","first_name":"Ting","last_name":"Wu"},{"full_name":"Xu, Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","first_name":"Shengduo","last_name":"Xu"},{"full_name":"Suo, Guoquan","first_name":"Guoquan","last_name":"Suo"},{"first_name":"Xiaohui","last_name":"Ye","full_name":"Ye, Xiaohui"},{"first_name":"Xiaojiang","last_name":"Hou","full_name":"Hou, Xiaojiang"},{"first_name":"Yanling","last_name":"Yang","full_name":"Yang, Yanling"},{"first_name":"Qingfeng","last_name":"Liu","full_name":"Liu, Qingfeng"},{"full_name":"Wang, Hongqiang","first_name":"Hongqiang","last_name":"Wang"}],"date_updated":"2023-08-14T11:47:06Z","date_created":"2023-01-12T11:55:02Z","volume":613,"year":"2023","acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","publication_status":"epub_ahead","department":[{"_id":"MaIb"}],"publisher":"Elsevier"},{"doi":"10.1007/s40072-022-00254-w","language":[{"iso":"eng"}],"external_id":{"arxiv":["2102.07452"],"isi":["000799715600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2194-0401"]},"month":"09","author":[{"full_name":"Clozeau, Nicolas","first_name":"Nicolas","last_name":"Clozeau","id":"fea1b376-906f-11eb-847d-b2c0cf46455b"}],"volume":11,"date_updated":"2023-08-14T11:51:47Z","date_created":"2021-10-23T10:50:22Z","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2023","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2023-08-14T11:51:04Z","date_published":"2023-09-01T00:00:00Z","citation":{"ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w","ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-022-00254-w.","mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w.","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378."},"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","page":"1254–1378","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2023-08-14T11:51:04Z","date_created":"2023-08-14T11:51:04Z","checksum":"f83dcaecdbd3ace862c4ed97a20e8501","success":1,"relation":"main_file","file_id":"14052","content_type":"application/pdf","file_size":1635193,"creator":"dernst","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10173","intvolume":" 11","ddc":["510"],"status":"public","title":"Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields","abstract":[{"lang":"eng","text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods."}],"type":"journal_article"},{"file_date_updated":"2023-08-14T12:47:32Z","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder"}],"volume":185,"date_updated":"2023-08-14T12:48:09Z","date_created":"2022-08-07T22:02:00Z","acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2023","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"publication_status":"published","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"month":"04","doi":"10.1007/s00440-022-01156-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000830344500001"],"arxiv":["2106.10200"]},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-08-14T12:47:32Z","date_created":"2023-08-14T12:47:32Z","success":1,"checksum":"b9247827dae5544d1d19c37abe547abc","file_id":"14054","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":782278,"file_name":"2023_ProbabilityTheory_Cipolloni.pdf","access_level":"open_access"}],"_id":"11741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 185","title":"Quenched universality for deformed Wigner matrices","status":"public","ddc":["510"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7.","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7"},"publication":"Probability Theory and Related Fields","page":"1183–1218","article_type":"original"},{"external_id":{"isi":["000914749700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"quality_controlled":"1","isi":1,"doi":"10.1021/acs.chemmater.2c03542","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5002"],"issn":["0897-4756"]},"month":"01","year":"2023","acknowledgement":"The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF).","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"publication_status":"published","author":[{"first_name":"Siqi","last_name":"Wang","full_name":"Wang, Siqi"},{"full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277"},{"full_name":"Bai, Shulin","first_name":"Shulin","last_name":"Bai"},{"full_name":"Qin, Bingchao","last_name":"Qin","first_name":"Bingchao"},{"full_name":"Zhu, Yingcai","first_name":"Yingcai","last_name":"Zhu"},{"first_name":"Shaoping","last_name":"Zhan","full_name":"Zhan, Shaoping"},{"first_name":"Junqing","last_name":"Zheng","full_name":"Zheng, Junqing"},{"last_name":"Tang","first_name":"Shuwei","full_name":"Tang, Shuwei"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"}],"volume":35,"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-14T12:57:44Z","file_date_updated":"2023-08-14T12:57:25Z","citation":{"chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.","mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.","short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763.","ista":"Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.","ieee":"S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542","ama":"Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542"},"publication":"Chemistry of Materials","page":"755-763","article_type":"original","date_published":"2023-01-24T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"24","_id":"12331","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","ddc":["540"],"title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","status":"public","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2961043,"creator":"dernst","file_name":"2023_ChemistryMaterials_Wang.pdf","access_level":"open_access","date_updated":"2023-08-14T12:57:25Z","date_created":"2023-08-14T12:57:25Z","checksum":"b21dca2aa7a80c068bc256bdd1fea9df","success":1,"relation":"main_file","file_id":"14055"}],"type":"journal_article","issue":"2","abstract":[{"text":"High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance.","lang":"eng"}]},{"month":"04","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-022-00394-9","isi":1,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"file_date_updated":"2022-08-29T11:23:15Z","ec_funded":1,"date_created":"2022-08-28T22:02:01Z","date_updated":"2023-08-14T12:51:25Z","volume":69,"author":[{"first_name":"Alan M","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M"},{"last_name":"Klute","first_name":"Fabian","full_name":"Klute, Fabian"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"last_name":"Vogtenhuber","first_name":"Birgit","full_name":"Vogtenhuber, Birgit"},{"full_name":"Seidel, Raimund","first_name":"Raimund","last_name":"Seidel"},{"first_name":"Tilo","last_name":"Wiedera","full_name":"Wiedera, Tilo"}],"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","article_type":"original","page":"745–770","publication":"Discrete and Computational Geometry","citation":{"chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9"},"abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","access_level":"open_access","creator":"alisjak","file_size":1002218,"content_type":"application/pdf","file_id":"12006","relation":"main_file","date_created":"2022-08-29T11:23:15Z","date_updated":"2022-08-29T11:23:15Z","success":1,"checksum":"def7ae3b28d9fd6aec16450e40090302"}],"ddc":["510"],"status":"public","title":"Inserting one edge into a simple drawing is hard","intvolume":" 69","_id":"11999","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12330","intvolume":" 36","status":"public","title":"The splay-list: A distribution-adaptive concurrent skip-list","abstract":[{"lang":"eng","text":"The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads."}],"type":"journal_article","date_published":"2023-09-01T00:00:00Z","citation":{"mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x.","short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418.","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x"},"publication":"Distributed Computing","page":"395-418","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"full_name":"Aksenov, Vitalii","first_name":"Vitalii","last_name":"Aksenov","id":"2980135A-F248-11E8-B48F-1D18A9856A87"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Drozdova, Alexandra","last_name":"Drozdova","first_name":"Alexandra"},{"full_name":"Mohtashami, Amirkeivan","last_name":"Mohtashami","first_name":"Amirkeivan"}],"volume":36,"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-14T12:54:32Z","year":"2023","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"publication_status":"published","doi":"10.1007/s00446-022-00441-x","language":[{"iso":"eng"}],"external_id":{"arxiv":["2008.01009"],"isi":["000913424000001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01009"}],"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"month":"09"},{"scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793."},"publication":"Molecular Ecology","page":"1441-1457","article_type":"original","date_published":"2023-03-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12159","intvolume":" 32","status":"public","ddc":["570"],"title":"On the origin and structure of haplotype blocks","file":[{"access_level":"open_access","file_name":"2023_MolecularEcology_Shipilina.pdf","creator":"dernst","file_size":7144607,"content_type":"application/pdf","file_id":"14062","relation":"main_file","success":1,"checksum":"b10e0f8fa3dc4d72aaf77a557200978a","date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z"}],"oa_version":"Published Version","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"oa":1,"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"isi":1,"quality_controlled":"1","doi":"10.1111/mec.16793","language":[{"iso":"eng"}],"file_date_updated":"2023-08-16T08:15:41Z","pmid":1,"year":"2023","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Shipilina, Daria","first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka"},{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"volume":32,"date_created":"2023-01-12T12:09:17Z","date_updated":"2023-08-16T08:18:47Z"},{"file_date_updated":"2023-08-16T09:36:28Z","article_number":"100079","author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"full_name":"Lebedenko, Olga O.","last_name":"Lebedenko","first_name":"Olga O."},{"full_name":"Becker, Lea Marie","last_name":"Becker","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"full_name":"Ayala, Isabel","first_name":"Isabel","last_name":"Ayala"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R.","last_name":"Skrynnikov"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"}],"date_created":"2023-01-12T11:55:38Z","date_updated":"2023-08-16T09:37:25Z","volume":7,"year":"2023","acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","pmid":1,"publication_status":"published","department":[{"_id":"PaSc"}],"publisher":"Elsevier","month":"01","publication_identifier":{"issn":["2590-1524"]},"doi":"10.1016/j.yjsbx.2022.100079","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["36578472"]},"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2023-08-16T09:36:28Z","date_updated":"2023-08-16T09:36:28Z","success":1,"checksum":"b4b1c10a31018aafe053b7d55a470e54","file_id":"14064","relation":"main_file","creator":"dernst","file_size":5132322,"content_type":"application/pdf","file_name":"2023_JourStrucBiologyX_Gauto.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12114","ddc":["570"],"title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","status":"public","intvolume":" 7","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["Structural Biology"],"date_published":"2023-01-01T00:00:00Z","publication":"Journal of Structural Biology: X","citation":{"chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079"},"article_type":"original"},{"issue":"6","abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_FEBSLetters_Loose.pdf","creator":"dernst","content_type":"application/pdf","file_size":3148143,"file_id":"14063","relation":"main_file","success":1,"checksum":"7492244d3f9c5faa1347ef03f6e5bc84","date_updated":"2023-08-16T08:31:04Z","date_created":"2023-08-16T08:31:04Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12163","intvolume":" 597","status":"public","ddc":["570"],"title":"In vitro reconstitution of small GTPase regulation","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"date_published":"2023-03-01T00:00:00Z","citation":{"short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777."},"publication":"FEBS Letters","page":"762-777","article_type":"review","file_date_updated":"2023-08-16T08:31:04Z","author":[{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"full_name":"Auer, Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3580-2906","first_name":"Albert","last_name":"Auer"},{"full_name":"Brognara, Gabriel","first_name":"Gabriel","last_name":"Brognara","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"id":"55380f95-15b2-11ec-abd3-aff8e230696b","last_name":"Budiman","first_name":"Hanifatul R","full_name":"Budiman, Hanifatul R"},{"last_name":"Kowalski","first_name":"Lukasz M","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","first_name":"Ivana"}],"volume":597,"date_updated":"2023-08-16T08:32:29Z","date_created":"2023-01-12T12:09:58Z","pmid":1,"year":"2023","acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","publisher":"Wiley","department":[{"_id":"MaLo"}],"publication_status":"published","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"month":"03","doi":"10.1002/1873-3468.14540","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"quality_controlled":"1","isi":1},{"author":[{"full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","first_name":"Mirza Ahad"},{"last_name":"Hendler","first_name":"Danny","full_name":"Hendler, Danny"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"},{"last_name":"Travers","first_name":"Corentin","full_name":"Travers, Corentin"}],"date_created":"2023-01-12T12:10:08Z","date_updated":"2023-08-16T08:39:36Z","volume":36,"year":"2023","acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","month":"03","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"doi":"10.1007/s00446-022-00439-5","language":[{"iso":"eng"}],"external_id":{"isi":["000890138700001"]},"oa":1,"main_file_link":[{"url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/","open_access":"1"}],"isi":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"type":"journal_article","oa_version":"Preprint","_id":"12164","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Long-lived counters with polylogarithmic amortized step complexity","intvolume":" 36","day":"01","article_processing_charge":"No","scopus_import":"1","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"date_published":"2023-03-01T00:00:00Z","publication":"Distributed Computing","citation":{"short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43."},"article_type":"original","page":"29-43"},{"quality_controlled":"1","doi":"10.1016/j.matpr.2022.11.037","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2214-7853"]},"year":"2023","publication_status":"published","publisher":"Elsevier","department":[{"_id":"BjHo"}],"author":[{"full_name":"Khatoon, Bushra","last_name":"Khatoon","first_name":"Bushra"},{"first_name":"Shoaib","last_name":"Kamil","id":"185a19af-dc7d-11ea-9b2f-8eb2201959e9","full_name":"Kamil, Shoaib"},{"first_name":"Hitesh","last_name":"Babu","full_name":"Babu, Hitesh"},{"first_name":"M.","last_name":"Siraj Alam","full_name":"Siraj Alam, M."}],"date_updated":"2023-08-16T09:08:11Z","date_created":"2023-01-12T12:11:26Z","volume":78,"publication":"Materials Today: Proceedings","citation":{"ista":"Khatoon B, Kamil S, Babu H, Siraj Alam M. 2023. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 78(Part 1), 40–47.","apa":"Khatoon, B., Kamil, S., Babu, H., & Siraj Alam, M. (2023). Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. Elsevier. https://doi.org/10.1016/j.matpr.2022.11.037","ieee":"B. Khatoon, S. Kamil, H. Babu, and M. Siraj Alam, “Experimental analysis of Cascade CSTRs with step and pulse inputs,” Materials Today: Proceedings, vol. 78, no. Part 1. Elsevier, pp. 40–47, 2023.","ama":"Khatoon B, Kamil S, Babu H, Siraj Alam M. Experimental analysis of Cascade CSTRs with step and pulse inputs. Materials Today: Proceedings. 2023;78(Part 1):40-47. doi:10.1016/j.matpr.2022.11.037","chicago":"Khatoon, Bushra, Shoaib Kamil, Hitesh Babu, and M. Siraj Alam. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings. Elsevier, 2023. https://doi.org/10.1016/j.matpr.2022.11.037.","mla":"Khatoon, Bushra, et al. “Experimental Analysis of Cascade CSTRs with Step and Pulse Inputs.” Materials Today: Proceedings, vol. 78, no. Part 1, Elsevier, 2023, pp. 40–47, doi:10.1016/j.matpr.2022.11.037.","short":"B. Khatoon, S. Kamil, H. Babu, M. Siraj Alam, Materials Today: Proceedings 78 (2023) 40–47."},"article_type":"original","page":"40-47","date_published":"2023-03-20T00:00:00Z","scopus_import":"1","keyword":["General Medicine"],"day":"20","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12172","status":"public","title":"Experimental analysis of Cascade CSTRs with step and pulse inputs","intvolume":" 78","oa_version":"None","type":"journal_article","abstract":[{"text":"In industrial reactors and equipment, non-ideality is quite a common phenomenon rather than an exception. These deviations from ideality impact the process's overall efficiency and the effectiveness of the equipment. To recognize the associated non-ideality, one needs to have enough understanding of the formulation of the equations and in-depth knowledge of the residence time distribution (RTD) data of real reactors. In the current work, step input and pulse input were used to create RTD data for Cascade continuous stirred tank reactors (CSTRs). For the aforementioned configuration, experiments were run at various flow rates to validate the developed characteristic equations. To produce RTD data, distilled water was utilized as the flowing fluid, and NaOH was the tracer substance. The ideal behavior of tracer concentration exits age distribution, and cumulative fraction for each setup and each input was plotted and experimental results were compared with perfect behavior. Deviation of concentration exit age distribution and cumulative fractional distribution from ideal behavior is more in pulse input as compared to a step input. For ideal cases, the exit age distribution curve and cumulative fraction curves are independent of the type of input. But a significant difference was observed for the two cases, which may be due to non-measurable fluctuations in volumetric flow rate, non-achievement of instant injection of tracer in case of pulse input, and slight variations in the sampling period. Further, with increasing flow rate, concentration, exit age, and cumulative fractional curves shifted upward, and this behavior matches with the actual case.","lang":"eng"}],"issue":"Part 1"},{"publication_identifier":{"eissn":["1662-5129"]},"month":"01","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36704406"],"isi":["000919786900001"]},"language":[{"iso":"eng"}],"doi":"10.3389/fnana.2022.1097467","article_number":"1097467","file_date_updated":"2023-02-06T07:56:14Z","publisher":"Frontiers","department":[{"_id":"PeJo"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","volume":16,"date_created":"2023-02-05T23:01:00Z","date_updated":"2023-08-16T11:37:52Z","author":[{"full_name":"Ortiz-Leal, Irene","last_name":"Ortiz-Leal","first_name":"Irene"},{"last_name":"Torres","first_name":"Mateo V.","full_name":"Torres, Mateo V."},{"full_name":"Vargas Barroso, Victor M","last_name":"Vargas Barroso","first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luis Eusebio","last_name":"Fidalgo","full_name":"Fidalgo, Luis Eusebio"},{"full_name":"López-Beceiro, Ana María","last_name":"López-Beceiro","first_name":"Ana María"},{"full_name":"Larriva-Sahd, Jorge A.","first_name":"Jorge A.","last_name":"Larriva-Sahd"},{"last_name":"Sánchez-Quinteiro","first_name":"Pablo","full_name":"Sánchez-Quinteiro, Pablo"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10","article_type":"original","citation":{"ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467","ieee":"I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467."},"publication":"Frontiers in Neuroanatomy","date_published":"2023-01-10T00:00:00Z","type":"journal_article","abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"intvolume":" 16","ddc":["570"],"status":"public","title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12515","file":[{"creator":"dernst","content_type":"application/pdf","file_size":21943473,"file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","access_level":"open_access","date_updated":"2023-02-06T07:56:14Z","date_created":"2023-02-06T07:56:14Z","success":1,"checksum":"49cd40f3bda6f267079427042e7d15e3","file_id":"12518","relation":"main_file"}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41587-022-01560-3","isi":1,"quality_controlled":"1","external_id":{"isi":["000909067600003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-16T11:32:33Z","volume":41,"author":[{"first_name":"Jake","last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake"},{"first_name":"Maria","last_name":"Florescu","full_name":"Florescu, Maria"},{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"full_name":"De Barbanson, Buys Anton","last_name":"De Barbanson","first_name":"Buys Anton"},{"full_name":"Wellenstein, Max D.","last_name":"Wellenstein","first_name":"Max D."},{"full_name":"Van Oudenaarden, Alexander","first_name":"Alexander","last_name":"Van Oudenaarden"}],"publication_status":"published","department":[{"_id":"ScienComp"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","file_date_updated":"2023-08-16T11:30:45Z","date_published":"2023-06-01T00:00:00Z","article_type":"original","page":"813–823","publication":"Nature Biotechnology","citation":{"ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023.","mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":12040976,"creator":"dernst","access_level":"open_access","file_name":"2023_NatureBioTech_Yeung.pdf","checksum":"668447a1c8d360b68f8aaf9e08ed644f","success":1,"date_updated":"2023-08-16T11:30:45Z","date_created":"2023-08-16T11:30:45Z","relation":"main_file","file_id":"14066"}],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","ddc":["570"],"status":"public","intvolume":" 41","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12106","abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"type":"journal_article"},{"publication_identifier":{"issn":["1424-0637"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1007/s00023-022-01252-3","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.15284"}],"external_id":{"arxiv":["2205.15284"],"isi":["000910751800002"]},"oa":1,"ec_funded":1,"volume":24,"date_created":"2023-01-15T23:00:52Z","date_updated":"2023-08-16T11:34:03Z","author":[{"first_name":"Chiara","last_name":"Boccato","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"department":[{"_id":"RoSe"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","page":"1505-1560","article_type":"original","citation":{"ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023.","apa":"Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3","chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560."},"publication":"Annales Henri Poincare","abstract":[{"text":"We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 24","title":"The Bose Gas in a box with Neumann boundary conditions","status":"public","_id":"12183","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"12544","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510","540"],"status":"public","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","intvolume":" 63","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14070","checksum":"7d20562269edff1e31b9d6019d4983b0","success":1,"date_created":"2023-08-16T12:21:13Z","date_updated":"2023-08-16T12:21:13Z","access_level":"open_access","file_name":"2023_JCIM_Koehl.pdf","file_size":8069223,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software.","lang":"eng"}],"issue":"3","publication":"Journal of Chemical Information and Modeling","citation":{"mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985.","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","apa":"Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346"},"article_type":"original","page":"973-985","date_published":"2023-02-13T00:00:00Z","scopus_import":"1","day":"13","article_processing_charge":"No","has_accepted_license":"1","year":"2023","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"HeEd"}],"author":[{"full_name":"Koehl, Patrice","first_name":"Patrice","last_name":"Koehl"},{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"date_updated":"2023-08-16T12:22:07Z","date_created":"2023-02-12T23:00:59Z","volume":63,"file_date_updated":"2023-08-16T12:21:13Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36638318"],"isi":["000920370700001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"doi":"10.1021/acs.jcim.2c01346","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1549-960X"],"issn":["1549-9596"]}}]