[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"title":"LightPIR: Privacy-preserving route discovery for payment channel networks","day":"21","department":[{"_id":"KrPi"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1861-2288"],"isbn":["978-1-6654-4501-6"],"eisbn":["978-3-9031-7639-3"]},"conference":{"name":"2021 IFIP Networking Conference (IFIP Networking)","end_date":"2021-06-24","location":"Espoo and Helsinki, Finland","start_date":"2021-06-21"},"doi":"10.23919/IFIPNetworking52078.2021.9472205","isi":1,"publisher":"IEEE","_id":"9969","date_published":"2021-06-21T00:00:00Z","quality_controlled":"1","year":"2021","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14506"}]},"month":"06","author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"first_name":"Iosif","last_name":"Salem","full_name":"Salem, Iosif"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0001-3676-4809","first_name":"Michelle X","last_name":"Yeo"}],"date_updated":"2026-04-07T13:29:44Z","arxiv":1,"project":[{"grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","date_created":"2021-08-29T22:01:16Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04293"}],"type":"conference","abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths.","lang":"eng"}],"status":"public","external_id":{"arxiv":["2104.04293"],"isi":["000853016800008"]},"citation":{"short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","mla":"Pietrzak, Krzysztof Z., et al. <i>LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks</i>. IEEE, 2021, doi:<a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">10.23919/IFIPNetworking52078.2021.9472205</a>.","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:<a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">10.23919/IFIPNetworking52078.2021.9472205</a>","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","apa":"Pietrzak, K. Z., Salem, I., Schmid, S., &#38; Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. <a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">https://doi.org/10.23919/IFIPNetworking52078.2021.9472205</a>","chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. <a href=\"https://doi.org/10.23919/IFIPNetworking52078.2021.9472205\">https://doi.org/10.23919/IFIPNetworking52078.2021.9472205</a>."},"ec_funded":1,"language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/4.0/","title":"Complete gradient estimates of quantum Markov semigroups","oa":1,"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"day":"30","department":[{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"file":[{"access_level":"open_access","relation":"main_file","creator":"cchlebak","date_created":"2021-09-08T07:34:24Z","content_type":"application/pdf","file_size":505971,"date_updated":"2021-09-08T09:46:34Z","file_id":"9990","file_name":"2021_CommunMathPhys_Wirth.pdf","checksum":"8a602f916b1c2b0dc1159708b7cb204b"}],"acknowledgement":"Both authors would like to thank Jan Maas for fruitful discussions and helpful comments.","isi":1,"doi":"10.1007/s00220-021-04199-4","publisher":"Springer Nature","_id":"9973","quality_controlled":"1","date_published":"2021-08-30T00:00:00Z","year":"2021","publication_status":"published","file_date_updated":"2021-09-08T09:46:34Z","volume":387,"month":"08","author":[{"orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"last_name":"Zhang","first_name":"Haonan","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"pmid":1,"page":"761–791","intvolume":"       387","ddc":["621"],"arxiv":1,"date_updated":"2025-06-12T06:30:13Z","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"corr_author":"1","type":"journal_article","date_created":"2021-08-30T10:07:44Z","publication":"Communications in Mathematical Physics","scopus_import":"1","oa_version":"Published Version","status":"public","external_id":{"arxiv":["2007.13506"],"pmid":["34776525"],"isi":["000691214200001"]},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors."}],"language":[{"iso":"eng"}],"citation":{"chicago":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-021-04199-4\">https://doi.org/10.1007/s00220-021-04199-4</a>.","apa":"Wirth, M., &#38; Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-021-04199-4\">https://doi.org/10.1007/s00220-021-04199-4</a>","ieee":"M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,” <i>Communications in Mathematical Physics</i>, vol. 387. Springer Nature, pp. 761–791, 2021.","ista":"Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791.","ama":"Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. 2021;387:761–791. doi:<a href=\"https://doi.org/10.1007/s00220-021-04199-4\">10.1007/s00220-021-04199-4</a>","mla":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>, vol. 387, Springer Nature, 2021, pp. 761–791, doi:<a href=\"https://doi.org/10.1007/s00220-021-04199-4\">10.1007/s00220-021-04199-4</a>.","short":"M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791."},"ec_funded":1,"article_type":"original"},{"related_material":{"record":[{"relation":"later_version","id":"10813","status":"public"}]},"month":"08","year":"2021","file_date_updated":"2021-08-31T14:02:19Z","publication_status":"submitted","page":"21","author":[{"last_name":"Cao","first_name":"Deqing","full_name":"Cao, Deqing"},{"last_name":"Shen","first_name":"Xiaoxiao","full_name":"Shen, Xiaoxiao"},{"first_name":"Aiping","last_name":"Wang","full_name":"Wang, Aiping"},{"last_name":"Yu","first_name":"Fengjiao","full_name":"Yu, Fengjiao"},{"last_name":"Wu","first_name":"Yuping","full_name":"Wu, Yuping"},{"full_name":"Shi, Siqi","last_name":"Shi","first_name":"Siqi"},{"orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"}],"ddc":["541"],"date_updated":"2024-10-09T21:01:46Z","language":[{"iso":"eng"}],"citation":{"short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.).","mla":"Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” <i>Research Square</i>, Research Square, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">10.21203/rs.3.rs-750965/v1</a>.","ieee":"D. Cao <i>et al.</i>, “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” <i>Research Square</i>. Research Square.","ama":"Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">10.21203/rs.3.rs-750965/v1</a>","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, <a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">10.21203/rs.3.rs-750965/v1</a>.","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. <i>Research Square</i>. Research Square. <a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">https://doi.org/10.21203/rs.3.rs-750965/v1</a>","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” <i>Research Square</i>. Research Square, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">https://doi.org/10.21203/rs.3.rs-750965/v1</a>."},"type":"preprint","corr_author":"1","publication":"Research Square","oa_version":"Preprint","date_created":"2021-08-31T12:54:16Z","has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents."}],"day":"18","keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"department":[{"_id":"StFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","oa":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2693-5015"]},"doi":"10.21203/rs.3.rs-750965/v1","file":[{"access_level":"open_access","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","date_created":"2021-08-31T14:02:19Z","file_size":1019662,"file_id":"9979","file_name":"2021_ResearchSquare_Cao.pdf","date_updated":"2021-08-31T14:02:19Z","success":1,"checksum":"1878e91c29d5769ed5a827b0b7addf00"}],"acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ","publisher":"Research Square","_id":"9978","date_published":"2021-08-18T00:00:00Z"},{"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge TU Graz for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University\r\n6 of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2-1863. S.A.F. is indebted to IST Austria for support. ","doi":"10.21203/rs.3.rs-818607/v1","date_updated":"2021-12-03T10:35:42Z","ddc":["621"],"citation":{"ama":"Prehal C, Talian SD, Vizintin A, et al. Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">10.21203/rs.3.rs-818607/v1</a>","ista":"Prehal C, Talian SD, Vizintin A, Amenitsch H, Dominko R, Freunberger SA, Wood V. Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. Research Square, <a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">10.21203/rs.3.rs-818607/v1</a>.","ieee":"C. Prehal <i>et al.</i>, “Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries,” <i>Research Square</i>. .","apa":"Prehal, C., Talian, S. D., Vizintin, A., Amenitsch, H., Dominko, R., Freunberger, S. A., &#38; Wood, V. (n.d.). Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">https://doi.org/10.21203/rs.3.rs-818607/v1</a>","short":"C. Prehal, S.D. Talian, A. Vizintin, H. Amenitsch, R. Dominko, S.A. Freunberger, V. Wood, Research Square (n.d.).","mla":"Prehal, Christian, et al. “Mechanism of Li2S Formation and Dissolution in Lithium-Sulphur Batteries.” <i>Research Square</i>, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">10.21203/rs.3.rs-818607/v1</a>.","chicago":"Prehal, Christian, Sara Drvarič Talian, Alen Vizintin, Heinz Amenitsch, Robert Dominko, Stefan Alexander Freunberger, and Vanessa Wood. “Mechanism of Li2S Formation and Dissolution in Lithium-Sulphur Batteries.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">https://doi.org/10.21203/rs.3.rs-818607/v1</a>."},"language":[{"iso":"eng"}],"_id":"9980","date_published":"2021-08-16T00:00:00Z","abstract":[{"text":"Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film.","lang":"eng"}],"status":"public","publication":"Research Square","date_created":"2021-09-02T08:45:00Z","oa_version":"Preprint","type":"preprint","main_file_link":[{"open_access":"1","url":"https://www.researchsquare.com/article/rs-818607/v1"}],"department":[{"_id":"StFr"}],"month":"08","keyword":["Li2S","Lithium Sulphur Batteries","SAXS","WAXS"],"day":"16","publication_status":"submitted","oa":1,"title":"Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries","year":"2021","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"21","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"first_name":"Sara Drvarič","last_name":"Talian","full_name":"Talian, Sara Drvarič"},{"last_name":"Vizintin","first_name":"Alen","full_name":"Vizintin, Alen"},{"first_name":"Heinz","last_name":"Amenitsch","full_name":"Amenitsch, Heinz"},{"full_name":"Dominko, Robert","last_name":"Dominko","first_name":"Robert"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"},{"first_name":"Vanessa","last_name":"Wood","full_name":"Wood, Vanessa"}]},{"date_updated":"2025-05-14T10:51:45Z","ddc":["519"],"arxiv":1,"intvolume":"        11","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"abstract":[{"lang":"eng","text":"The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions\r\nfor further developments."}],"external_id":{"arxiv":["2103.16468"],"isi":["000692534200001"]},"status":"public","has_accepted_license":"1","oa_version":"Published Version","date_created":"2021-09-02T11:49:47Z","scopus_import":"1","publication":"SciPost Physics","type":"journal_article","ec_funded":1,"article_type":"original","citation":{"chicago":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">https://doi.org/10.21468/scipostphys.11.3.048</a>.","short":"S. De Nicola, SciPost Physics 11 (2021).","mla":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” <i>SciPost Physics</i>, vol. 11, no. 3, 048, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">10.21468/scipostphys.11.3.048</a>.","ieee":"S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” <i>SciPost Physics</i>, vol. 11, no. 3. SciPost Foundation, 2021.","ama":"De Nicola S. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. <i>SciPost Physics</i>. 2021;11(3). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">10.21468/scipostphys.11.3.048</a>","ista":"De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 11(3), 048.","apa":"De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation of quantum spin dynamics. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">https://doi.org/10.21468/scipostphys.11.3.048</a>"},"language":[{"iso":"eng"}],"publication_status":"published","file_date_updated":"2021-09-02T14:05:43Z","year":"2021","month":"09","issue":"3","volume":11,"author":[{"orcid":"0000-0002-4842-6671","first_name":"Stefano","last_name":"De Nicola","full_name":"De Nicola, Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87"}],"publisher":"SciPost Foundation","isi":1,"file":[{"date_created":"2021-09-02T14:05:43Z","content_type":"application/pdf","creator":"cchlebak","relation":"main_file","access_level":"open_access","checksum":"e4ec69d893e31811efc6093cb6ea8eb7","success":1,"file_id":"9984","file_name":"2021_SciPostPhys_DeNicola.pdf","date_updated":"2021-09-02T14:05:43Z","file_size":373833}],"doi":"10.21468/scipostphys.11.3.048","article_number":"048","date_published":"2021-09-02T00:00:00Z","_id":"9981","quality_controlled":"1","oa":1,"title":"Importance sampling scheme for the stochastic simulation of quantum spin dynamics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaSe"}],"keyword":["General Physics and Astronomy"],"day":"02","publication_identifier":{"issn":["2542-4653"],"eissn":["2666-9366"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No"},{"pmid":1,"author":[{"last_name":"Watson","orcid":"0000-0002-8698-3823","first_name":"Jake","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"first_name":"Alexandra","last_name":"Pinggera","full_name":"Pinggera, Alexandra"},{"full_name":"Ho, Hinze","last_name":"Ho","first_name":"Hinze"},{"last_name":"Greger","first_name":"Ingo H.","full_name":"Greger, Ingo H."}],"volume":12,"issue":"1","month":"08","year":"2021","file_date_updated":"2021-09-08T12:57:06Z","publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” <i>Nature Communications</i>. Nature Publishing Group, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25281-4\">https://doi.org/10.1038/s41467-021-25281-4</a>.","mla":"Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” <i>Nature Communications</i>, vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25281-4\">10.1038/s41467-021-25281-4</a>.","short":"J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).","apa":"Watson, J., Pinggera, A., Ho, H., &#38; Greger, I. H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-021-25281-4\">https://doi.org/10.1038/s41467-021-25281-4</a>","ista":"Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 12(1), 5083.","ieee":"J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Publishing Group, 2021.","ama":"Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-25281-4\">10.1038/s41467-021-25281-4</a>"},"type":"journal_article","publication":"Nature Communications","oa_version":"Published Version","date_created":"2021-09-05T22:01:23Z","scopus_import":"1","status":"public","external_id":{"isi":["000687672000006"],"pmid":["34426577 "]},"has_accepted_license":"1","abstract":[{"text":"AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity.","lang":"eng"}],"intvolume":"        12","ddc":["612"],"date_updated":"2023-08-11T11:07:51Z","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2041-1723"]},"day":"23","department":[{"_id":"PeJo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions","oa":1,"_id":"9985","date_published":"2021-08-23T00:00:00Z","quality_controlled":"1","article_number":"5083","file":[{"content_type":"application/pdf","date_created":"2021-09-08T12:57:06Z","access_level":"open_access","creator":"cchlebak","relation":"main_file","file_id":"9991","file_name":"2021_NatureCommunications_Watson.pdf","date_updated":"2021-09-08T12:57:06Z","checksum":"1bf4f6a561f96bc426d754de9cb57710","success":1,"file_size":18310502}],"doi":"10.1038/s41467-021-25281-4","acknowledgement":"The authors are very grateful to Andrew Penn for advice and discussions on surface receptor labelling in slice tissue, dissociated culture transfection, and for providing tdTomato and BirAER expression plasmids. This work would not have been possible without support from the Biological Services teams at both the Laboratory of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression constructs, Veronica Chang for assistance with scFv-Clasp protein production, and Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa and Ole Paulsen for critical reading of the manuscript and constructive feedback. This work was supported by grants from the Medical Research Council (MC_U105174197) and BBSRC (BB/N002113/1).","isi":1,"publisher":"Nature Publishing Group"},{"ddc":["575"],"date_updated":"2024-10-09T21:00:50Z","intvolume":"        22","has_accepted_license":"1","status":"public","external_id":{"isi":["000694347100001"],"pmid":["34502129"]},"abstract":[{"lang":"eng","text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth."}],"corr_author":"1","type":"journal_article","oa_version":"Published Version","date_created":"2021-09-05T22:01:24Z","scopus_import":"1","publication":"International Journal of Molecular Sciences","language":[{"iso":"eng"}],"article_type":"original","citation":{"short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 17, 9222, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22179222\">10.3390/ijms22179222</a>.","ieee":"S. M. Velasquez <i>et al.</i>, “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 17. MDPI, 2021.","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. <i>International Journal of Molecular Sciences</i>. 2021;22(17). doi:<a href=\"https://doi.org/10.3390/ijms22179222\">10.3390/ijms22179222</a>","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22179222\">https://doi.org/10.3390/ijms22179222</a>","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22179222\">https://doi.org/10.3390/ijms22179222</a>."},"publication_status":"published","file_date_updated":"2021-09-07T09:04:53Z","year":"2021","month":"08","volume":22,"issue":"17","author":[{"full_name":"Velasquez, Silvia Melina","last_name":"Velasquez","first_name":"Silvia Melina"},{"full_name":"Guo, Xiaoyuan","first_name":"Xiaoyuan","last_name":"Guo"},{"last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"full_name":"Aryal, Bibek","first_name":"Bibek","last_name":"Aryal"},{"last_name":"Venhuizen","first_name":"Peter","full_name":"Venhuizen, Peter"},{"full_name":"Barbez, Elke","first_name":"Elke","last_name":"Barbez"},{"first_name":"Kai Alexander","last_name":"Dünser","full_name":"Dünser, Kai Alexander"},{"first_name":"Martin","last_name":"Darino","full_name":"Darino, Martin"},{"last_name":"Pӗnčík","first_name":"Aleš","full_name":"Pӗnčík, Aleš"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"},{"first_name":"Gregory","last_name":"Mouille","full_name":"Mouille, Gregory"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bhalerao, Rishikesh P.","first_name":"Rishikesh P.","last_name":"Bhalerao"},{"first_name":"Jozef","last_name":"Mravec","full_name":"Mravec, Jozef"},{"last_name":"Kleine-Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"}],"pmid":1,"publisher":"MDPI","file":[{"date_created":"2021-09-06T12:50:19Z","content_type":"application/pdf","creator":"cchlebak","relation":"main_file","access_level":"open_access","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","file_id":"9988","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","date_updated":"2021-09-07T09:04:53Z","file_size":2162247}],"acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","doi":"10.3390/ijms22179222","isi":1,"article_number":"9222","quality_controlled":"1","_id":"9986","date_published":"2021-08-26T00:00:00Z","title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EvBe"}],"day":"26","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"article_processing_charge":"Yes"},{"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eisbn":["978-3-030-81685-8"],"issn":["0302-9743"],"isbn":["978-3-030-81684-1"],"eissn":["1611-3349"]},"day":"15","department":[{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Stateless model checking under a reads-value-from equivalence","oa":1,"quality_controlled":"1","_id":"9987","date_published":"2021-07-15T00:00:00Z","doi":"10.1007/978-3-030-81685-8_16","isi":1,"acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) through project ICT15-003.","file":[{"creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_created":"2022-05-13T07:00:20Z","file_size":1516756,"checksum":"4b346e5fbaa8b9bdf107819c7b2aadee","success":1,"file_name":"2021_LNCS_Agarwal.pdf","file_id":"11368","date_updated":"2022-05-13T07:00:20Z"}],"publisher":"Springer Nature","conference":{"name":"CAV: Computer Aided Verification ","start_date":"2021-07-20","location":"Virtual","end_date":"2021-07-23"},"page":"341-366","alternative_title":["LNCS"],"author":[{"full_name":"Agarwal, Pratyush","first_name":"Pratyush","last_name":"Agarwal"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Shreya","last_name":"Pathak","full_name":"Pathak, Shreya"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"volume":"12759 ","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"month":"07","year":"2021","publication_status":"published","file_date_updated":"2022-05-13T07:00:20Z","language":[{"iso":"eng"}],"citation":{"short":"P. Agarwal, K. Chatterjee, S. Pathak, A. Pavlogiannis, V. Toman, in:, 33rd International Conference on Computer-Aided Verification , Springer Nature, 2021, pp. 341–366.","mla":"Agarwal, Pratyush, et al. “Stateless Model Checking under a Reads-Value-from Equivalence.” <i>33rd International Conference on Computer-Aided Verification </i>, vol. 12759, Springer Nature, 2021, pp. 341–66, doi:<a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">10.1007/978-3-030-81685-8_16</a>.","ista":"Agarwal P, Chatterjee K, Pathak S, Pavlogiannis A, Toman V. 2021. Stateless model checking under a reads-value-from equivalence. 33rd International Conference on Computer-Aided Verification . CAV: Computer Aided Verification , LNCS, vol. 12759, 341–366.","ama":"Agarwal P, Chatterjee K, Pathak S, Pavlogiannis A, Toman V. Stateless model checking under a reads-value-from equivalence. In: <i>33rd International Conference on Computer-Aided Verification </i>. Vol 12759. Springer Nature; 2021:341-366. doi:<a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">10.1007/978-3-030-81685-8_16</a>","ieee":"P. Agarwal, K. Chatterjee, S. Pathak, A. Pavlogiannis, and V. Toman, “Stateless model checking under a reads-value-from equivalence,” in <i>33rd International Conference on Computer-Aided Verification </i>, Virtual, 2021, vol. 12759, pp. 341–366.","apa":"Agarwal, P., Chatterjee, K., Pathak, S., Pavlogiannis, A., &#38; Toman, V. (2021). Stateless model checking under a reads-value-from equivalence. In <i>33rd International Conference on Computer-Aided Verification </i> (Vol. 12759, pp. 341–366). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">https://doi.org/10.1007/978-3-030-81685-8_16</a>","chicago":"Agarwal, Pratyush, Krishnendu Chatterjee, Shreya Pathak, Andreas Pavlogiannis, and Viktor Toman. “Stateless Model Checking under a Reads-Value-from Equivalence.” In <i>33rd International Conference on Computer-Aided Verification </i>, 12759:341–66. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">https://doi.org/10.1007/978-3-030-81685-8_16</a>."},"ec_funded":1,"type":"conference","corr_author":"1","scopus_import":"1","publication":"33rd International Conference on Computer-Aided Verification ","date_created":"2021-09-05T22:01:24Z","oa_version":"Published Version","external_id":{"isi":["000698732400016"],"arxiv":["2105.06424"]},"status":"public","has_accepted_license":"1","abstract":[{"text":"Stateless model checking (SMC) is one of the standard approaches to the verification of concurrent programs. As scheduling non-determinism creates exponentially large spaces of thread interleavings, SMC attempts to partition this space into equivalence classes and explore only a few representatives from each class. The efficiency of this approach depends on two factors: (a) the coarseness of the partitioning, and (b) the time to generate representatives in each class. For this reason, the search for coarse partitionings that are efficiently explorable is an active research challenge. In this work we present   RVF-SMC , a new SMC algorithm that uses a novel reads-value-from (RVF) partitioning. Intuitively, two interleavings are deemed equivalent if they agree on the value obtained in each read event, and read events induce consistent causal orderings between them. The RVF partitioning is provably coarser than recent approaches based on Mazurkiewicz and “reads-from” partitionings. Our experimental evaluation reveals that RVF is quite often a very effective equivalence, as the underlying partitioning is exponentially coarser than other approaches. Moreover,   RVF-SMC  generates representatives very efficiently, as the reduction in the partitioning is often met with significant speed-ups in the model checking task.","lang":"eng"}],"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"arxiv":1,"ddc":["000"],"date_updated":"2026-04-08T07:00:30Z"},{"publisher":"Springer Nature","file":[{"file_size":584648,"success":1,"checksum":"beadc5a722ffb48190e1e63ee2dbfee5","date_updated":"2021-09-13T11:31:34Z","file_name":"2021_SelectaMath_Koroteev.pdf","file_id":"10010","relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","date_created":"2021-09-13T11:31:34Z"}],"acknowledgement":"First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s00029-021-00698-3","isi":1,"article_number":"87","quality_controlled":"1","_id":"9998","date_published":"2021-08-30T00:00:00Z","oa":1,"title":"Quantum K-theory of quiver varieties and many-body systems","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"day":"30","publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","date_updated":"2025-04-15T06:53:09Z","ddc":["530"],"intvolume":"        27","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"lang":"eng","text":"We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["000692795200001"]},"oa_version":"Published Version","date_created":"2021-09-12T22:01:22Z","scopus_import":"1","publication":"Selecta Mathematica","type":"journal_article","citation":{"chicago":"Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021).","mla":"Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>, vol. 27, no. 5, 87, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>.","ieee":"P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” <i>Selecta Mathematica</i>, vol. 27, no. 5. Springer Nature, 2021.","ama":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. 2021;27(5). doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>","ista":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87.","apa":"Koroteev, P., Pushkar, P., Smirnov, A. V., &#38; Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>"},"article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2021-09-13T11:31:34Z","publication_status":"published","year":"2021","month":"08","issue":"5","volume":27,"author":[{"full_name":"Koroteev, Peter","first_name":"Peter","last_name":"Koroteev"},{"first_name":"Petr","last_name":"Pushkar","id":"151DCEB6-9EC3-11E9-8480-ABECE5697425","full_name":"Pushkar, Petr"},{"first_name":"Andrey V.","last_name":"Smirnov","full_name":"Smirnov, Andrey V."},{"first_name":"Anton M.","last_name":"Zeitlin","full_name":"Zeitlin, Anton M."}]},{"file":[{"file_name":"2021_eLife_Pulgar.pdf","file_id":"11371","date_updated":"2022-05-13T08:03:37Z","checksum":"a3f82b0499cc822ac1eab48a01f3f57e","success":1,"file_size":9010446,"date_created":"2022-05-13T08:03:37Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"doi":"10.7554/eLife.66483","isi":1,"publisher":"eLife Sciences Publications","date_published":"2021-08-27T00:00:00Z","_id":"9999","quality_controlled":"1","article_number":"e66483","day":"27","keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"department":[{"_id":"CaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","oa":1,"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2050-084X"]},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"intvolume":"        10","ddc":["570"],"date_updated":"2025-04-14T07:46:58Z","language":[{"iso":"eng"}],"citation":{"chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>.","apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>","ieee":"E. Pulgar <i>et al.</i>, “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>","ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>, vol. 10, e66483, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021)."},"ec_funded":1,"article_type":"original","type":"journal_article","date_created":"2021-09-12T22:01:23Z","oa_version":"Published Version","scopus_import":"1","publication":"eLife","has_accepted_license":"1","external_id":{"isi":["000700428500001"],"pmid":["34448451"]},"status":"public","abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}],"volume":10,"month":"08","year":"2021","file_date_updated":"2022-05-13T08:03:37Z","publication_status":"published","pmid":1,"author":[{"full_name":"Pulgar, Eduardo","first_name":"Eduardo","last_name":"Pulgar"},{"last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia"},{"last_name":"Guerrero","first_name":"Néstor","full_name":"Guerrero, Néstor"},{"first_name":"Loreto","last_name":"López","full_name":"López, Loreto"},{"full_name":"Márquez, Susana","last_name":"Márquez","first_name":"Susana"},{"full_name":"Härtel, Steffen","last_name":"Härtel","first_name":"Steffen"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"},{"full_name":"Heisenberg, Carl Philipp","last_name":"Heisenberg","first_name":"Carl Philipp"},{"first_name":"Miguel L.","last_name":"Concha","full_name":"Concha, Miguel L."}]},{"language":[{"iso":"eng"}],"citation":{"chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ke Xiao, Mehran Nabahat, Jordi Arbiol, Jordi Llorca, Maria Ibáñez, and Andreu Cabot. “PbS–Pb–CuxS Composites for Thermoelectric Application.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsami.1c15609\">https://doi.org/10.1021/acsami.1c15609</a>.","short":"M. Li, Y. Liu, Y. Zhang, X. Han, K. Xiao, M. Nabahat, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 13 (2021) 51373–51382.","mla":"Li, Mengyao, et al. “PbS–Pb–CuxS Composites for Thermoelectric Application.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 43, American Chemical Society, 2021, pp. 51373–51382, doi:<a href=\"https://doi.org/10.1021/acsami.1c15609\">10.1021/acsami.1c15609</a>.","ieee":"M. Li <i>et al.</i>, “PbS–Pb–CuxS composites for thermoelectric application,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 43. American Chemical Society, pp. 51373–51382, 2021.","ama":"Li M, Liu Y, Zhang Y, et al. PbS–Pb–CuxS composites for thermoelectric application. <i>ACS Applied Materials and Interfaces</i>. 2021;13(43):51373–51382. doi:<a href=\"https://doi.org/10.1021/acsami.1c15609\">10.1021/acsami.1c15609</a>","ista":"Li M, Liu Y, Zhang Y, Han X, Xiao K, Nabahat M, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2021. PbS–Pb–CuxS composites for thermoelectric application. ACS Applied Materials and Interfaces. 13(43), 51373–51382.","apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Xiao, K., Nabahat, M., … Cabot, A. (2021). PbS–Pb–CuxS composites for thermoelectric application. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.1c15609\">https://doi.org/10.1021/acsami.1c15609</a>"},"ec_funded":1,"article_type":"original","main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/2117/363528/1/Pb%20mengyao.pdf","open_access":"1"}],"corr_author":"1","type":"journal_article","scopus_import":"1","oa_version":"Submitted Version","publication":"ACS Applied Materials and Interfaces","date_created":"2021-11-21T23:01:30Z","external_id":{"isi":["000715852100070"],"pmid":["34665616"]},"status":"public","abstract":[{"lang":"eng","text":"Composite materials offer numerous advantages in a wide range of applications, including thermoelectrics. Here, semiconductor–metal composites are produced by just blending nanoparticles of a sulfide semiconductor obtained in aqueous solution and at room temperature with a metallic Cu powder. The obtained blend is annealed in a reducing atmosphere and afterward consolidated into dense polycrystalline pellets through spark plasma sintering (SPS). We observe that, during the annealing process, the presence of metallic copper activates a partial reduction of the PbS, resulting in the formation of PbS–Pb–CuxS composites. The presence of metallic lead during the SPS process habilitates the liquid-phase sintering of the composite. Besides, by comparing the transport properties of PbS, the PbS–Pb–CuxS composites, and PbS–CuxS composites obtained by blending PbS and CuxS nanoparticles, we demonstrate that the presence of metallic lead decisively contributes to a strong increase of the charge carrier concentration through spillover of charge carriers enabled by the low work function of lead. The increase in charge carrier concentration translates into much higher electrical conductivities and moderately lower Seebeck coefficients. These properties translate into power factors up to 2.1 mW m–1 K–2 at ambient temperature, well above those of PbS and PbS + CuxS. Additionally, the presence of multiple phases in the final composite results in a notable decrease in the lattice thermal conductivity. Overall, the introduction of metallic copper in the initial blend results in a significant improvement of the thermoelectric performance of PbS, reaching a dimensionless thermoelectric figure of merit ZT = 1.1 at 750 K, which represents about a 400% increase over bare PbS. Besides, an average ZTave = 0.72 in the temperature range 320–773 K is demonstrated."}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"intvolume":"        13","date_updated":"2026-07-06T12:15:05Z","pmid":1,"page":"51373–51382","author":[{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740","first_name":"Yu"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Han, Xu","first_name":"Xu","last_name":"Han"},{"full_name":"Xiao, Ke","first_name":"Ke","last_name":"Xiao"},{"full_name":"Nabahat, Mehran","first_name":"Mehran","last_name":"Nabahat"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"volume":13,"issue":"43","month":"10","year":"2021","publication_status":"published","_id":"10327","date_published":"2021-10-19T00:00:00Z","quality_controlled":"1","das_tickbox":"1","acknowledgement":"This work was supported by the European Regional Development Funds. M.L., Y.Z., X.H., and K.X. thank the China Scholarship Council for scholarship support. M. I. has been financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. J.L. is a Serra Húnter fellow and is grateful to ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO project NANOGEN (PID2020-116093RB-C43). ICN2 was supported by the Severo Ochoa program from Spanish MINECO (grant no. SEV-2017-0706) and was funded by the CERCA Programme/Generalitat de Catalunya. X.H. thanks China Scholarship Council for scholarship support (201804910551). Part of the present work was performed in the framework of Universitat Autònoma de Barcelona Materials Science Ph.D. program.","doi":"10.1021/acsami.1c15609","isi":1,"publisher":"American Chemical Society","article_processing_charge":"No","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"keyword":["CuxS","PbS","energy conversion","nanocomposite","nanoparticle","solution synthesis","thermoelectric"],"day":"19","department":[{"_id":"MaIb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"PbS–Pb–CuxS composites for thermoelectric application","oa":1},{"pmid":1,"page":"4967–4978","author":[{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"orcid":"0000-0001-7313-6740","first_name":"Yu","last_name":"Liu","full_name":"Liu, Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"full_name":"Han, Xu","last_name":"Han","first_name":"Xu"},{"last_name":"Zhang","first_name":"Ting","full_name":"Zhang, Ting"},{"last_name":"Zuo","first_name":"Yong","full_name":"Zuo, Yong"},{"full_name":"Xie, Chenyang","first_name":"Chenyang","last_name":"Xie"},{"full_name":"Xiao, Ke","first_name":"Ke","last_name":"Xiao"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Llorca","first_name":"Jordi","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"},{"last_name":"Liu","first_name":"Junfeng","full_name":"Liu, Junfeng"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"volume":15,"issue":"3","month":"03","year":"2021","publication_status":"published","language":[{"iso":"eng"}],"citation":{"apa":"Li, M., Liu, Y., Zhang, Y., Han, X., Zhang, T., Zuo, Y., … Cabot, A. (2021). Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.0c09866\">https://doi.org/10.1021/acsnano.0c09866</a>","ama":"Li M, Liu Y, Zhang Y, et al. Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. <i>ACS Nano</i>. 2021;15(3):4967–4978. doi:<a href=\"https://doi.org/10.1021/acsnano.0c09866\">10.1021/acsnano.0c09866</a>","ista":"Li M, Liu Y, Zhang Y, Han X, Zhang T, Zuo Y, Xie C, Xiao K, Arbiol J, Llorca J, Ibáñez M, Liu J, Cabot A. 2021. Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide. ACS Nano. 15(3), 4967–4978.","ieee":"M. Li <i>et al.</i>, “Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide,” <i>ACS Nano</i>, vol. 15, no. 3. American Chemical Society, pp. 4967–4978, 2021.","mla":"Li, Mengyao, et al. “Effect of the Annealing Atmosphere on Crystal Phase and Thermoelectric Properties of Copper Sulfide.” <i>ACS Nano</i>, vol. 15, no. 3, American Chemical Society, 2021, pp. 4967–4978, doi:<a href=\"https://doi.org/10.1021/acsnano.0c09866\">10.1021/acsnano.0c09866</a>.","short":"M. Li, Y. Liu, Y. Zhang, X. Han, T. Zhang, Y. Zuo, C. Xie, K. Xiao, J. Arbiol, J. Llorca, M. Ibáñez, J. Liu, A. Cabot, ACS Nano 15 (2021) 4967–4978.","chicago":"Li, Mengyao, Yu Liu, Yu Zhang, Xu Han, Ting Zhang, Yong Zuo, Chenyang Xie, et al. “Effect of the Annealing Atmosphere on Crystal Phase and Thermoelectric Properties of Copper Sulfide.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.0c09866\">https://doi.org/10.1021/acsnano.0c09866</a>."},"article_type":"original","corr_author":"1","main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/handle/2117/363528/Pb%20mengyao.pdf?sequence=1&isAllowed=y","open_access":"1"}],"type":"journal_article","publication":"ACS Nano","oa_version":"Submitted Version","date_created":"2021-03-10T20:12:45Z","scopus_import":"1","external_id":{"isi":["000634569100106"],"pmid":["33645986"]},"status":"public","abstract":[{"lang":"eng","text":"Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies."}],"intvolume":"        15","date_updated":"2026-07-06T12:15:39Z","article_processing_charge":"No","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"day":"01","keyword":["General Engineering","General Physics and Astronomy","General Materials Science"],"department":[{"_id":"MaIb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide","oa":1,"_id":"9235","quality_controlled":"1","date_published":"2021-03-01T00:00:00Z","das_tickbox":"1","isi":1,"acknowledgement":"This work was supported by the European Regional Development Funds. M.Y.L., X.H., T.Z., and K.X. thank the China Scholarship Council for scholarship support. M.I. acknowledges financial support from IST Austria. J.L. acknowledges support from the National Natural Science Foundation of China (No. 22008091), the funding for scientific research startup of Jiangsu University (No. 19JDG044), and Jiangsu Provincial Program for High-Level Innovative and Entrepreneurial Talents Introduction. J.L. is a Serra Húnter fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER RTI2018-093996-B-C31 and GC 2017 SGR 128. ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327 and the Spanish MINECO ENE2017-85087-C3. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. T.Z. has received funding from the CSC-UAB PhD scholarship program.","doi":"10.1021/acsnano.0c09866","publisher":"American Chemical Society"},{"_id":"10134","quality_controlled":"1","date_published":"2021-10-12T00:00:00Z","article_number":"160602","das_tickbox":"1","isi":1,"doi":"10.1103/physrevlett.127.160602","acknowledgement":"We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez. F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z. is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program. R. V. K. is supported by NSERC of Canada.\r\n","publisher":"American Physical Society","article_processing_charge":"No","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"keyword":["General Physics and Astronomy"],"day":"12","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Anderson localization of composite particles","ec_funded":1,"article_type":"original","citation":{"chicago":"Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>.","ista":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite particles. Physical Review Letters. 127(16), 160602.","ieee":"F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization of composite particles,” <i>Physical Review Letters</i>, vol. 127, no. 16. American Physical Society, 2021.","ama":"Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite particles. <i>Physical Review Letters</i>. 2021;127(16). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>","apa":"Suzuki, F., Lemeshko, M., Zurek, W. H., &#38; Krems, R. V. (2021). Anderson localization of composite particles. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.160602\">https://doi.org/10.1103/physrevlett.127.160602</a>","short":"F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127 (2021).","mla":"Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” <i>Physical Review Letters</i>, vol. 127, no. 16, 160602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.160602\">10.1103/physrevlett.127.160602</a>."},"language":[{"iso":"eng"}],"date_created":"2021-10-13T09:21:33Z","publication":"Physical Review Letters","oa_version":"Preprint","scopus_import":"1","corr_author":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.06279"}],"abstract":[{"lang":"eng","text":"We investigate the effect of coupling between translational and internal degrees of freedom of composite quantum particles on their localization in a random potential. We show that entanglement between the two degrees of freedom weakens localization due to the upper bound imposed on the inverse participation ratio by purity of a quantum state. We perform numerical calculations for a two-particle system bound by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered lattice. We illustrate that the coupling has a dramatic effect on localization properties, even with a small number of internal states participating in quantum dynamics."}],"status":"public","external_id":{"isi":["000707495700001"],"arxiv":["2011.06279"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"intvolume":"       127","date_updated":"2026-07-06T12:22:26Z","arxiv":1,"author":[{"last_name":"Suzuki","first_name":"Fumika","orcid":"0000-0003-4982-5970","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","full_name":"Suzuki, Fumika"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zurek, Wojciech H.","first_name":"Wojciech H.","last_name":"Zurek"},{"last_name":"Krems","first_name":"Roman V.","full_name":"Krems, Roman V."}],"issue":"16","volume":127,"month":"10","year":"2021","publication_status":"published"},{"doi":"10.1371/journal.pcbi.1008529","isi":1,"file":[{"content_type":"application/pdf","date_created":"2021-02-04T12:30:48Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"e29f2b42651bef8e034781de8781ffac","success":1,"file_id":"9092","file_name":"2021_PlosComBio_Kavcic.pdf","date_updated":"2021-02-04T12:30:48Z","file_size":3690053}],"acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","publisher":"Public Library of Science","_id":"8997","date_published":"2021-01-07T00:00:00Z","quality_controlled":"1","article_number":"e1008529","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"day":"07","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Minimal biophysical model of combined antibiotic action","article_processing_charge":"Yes","publication_identifier":{"issn":["1553-7358"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27201-B22"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"intvolume":"        17","date_updated":"2026-07-06T12:44:35Z","ddc":["570"],"article_type":"original","citation":{"mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>."},"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"PLOS Computational Biology","scopus_import":"1","date_created":"2021-01-08T07:16:18Z","type":"journal_article","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"has_accepted_license":"1","external_id":{"pmid":["33411759"],"isi":["000608045000010"]},"status":"public","related_material":{"record":[{"status":"public","id":"8930","relation":"research_data"},{"relation":"earlier_version","id":"7673","status":"public"}]},"volume":17,"month":"01","year":"2021","publication_status":"published","file_date_updated":"2021-02-04T12:30:48Z","pmid":1,"author":[{"first_name":"Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"first_name":"Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}]},{"citation":{"chicago":"Anderson, Donovan J., Florian Pauler, Aaron McKenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>.","apa":"Anderson, D. J., Pauler, F., McKenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (n.d.). Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2020.12.31.425016\">https://doi.org/10.1101/2020.12.31.425016</a>","ista":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. bioRxiv, <a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","ieee":"D. J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous identification of brain cell type and lineage via single cell RNA sequencing,” <i>bioRxiv</i>. .","ama":"Anderson DJ, Pauler F, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous identification of brain cell type and lineage via single cell RNA sequencing. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>","mla":"Anderson, Donovan J., et al. “Simultaneous Identification of Brain Cell Type and Lineage via Single Cell RNA Sequencing.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2020.12.31.425016\">10.1101/2020.12.31.425016</a>.","short":"D.J. Anderson, F. Pauler, A. McKenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, BioRxiv (n.d.)."},"ec_funded":1,"language":[{"iso":"eng"}],"_id":"9082","date_published":"2021-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans."}],"das_tickbox":"1","status":"public","publication":"bioRxiv","date_created":"2021-02-04T07:23:23Z","oa_version":"Preprint","type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2020.12.31.425016","open_access":"1"}],"acknowledgement":"We thank Bill Bolosky, Microsoft Research, for earlier work showing proof of concept in TCGA\r\nbulk RNA-seq data. Supported by the Paul G. Allen Frontiers Group (University of Washington);\r\nNIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant\r\n(C13-002) to SH, and the European Research Council (ERC) under the European Union’s\r\nHorizon 2020 research and innovation program 725780 LinPro to SH.","project":[{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"doi":"10.1101/2020.12.31.425016","date_updated":"2026-07-06T12:46:11Z","article_processing_charge":"No","author":[{"full_name":"Anderson, Donovan J.","last_name":"Anderson","first_name":"Donovan J."},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler"},{"full_name":"McKenna, Aaron","first_name":"Aaron","last_name":"McKenna"},{"first_name":"Jay","last_name":"Shendure","full_name":"Shendure, Jay"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"department":[{"_id":"SiHi"}],"month":"01","day":"01","oa":1,"publication_status":"submitted","title":"Simultaneous identification of brain cell type and lineage via single cell RNA sequencing","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"status":"public","external_id":{"isi":["000720259500002"]},"has_accepted_license":"1","oa_version":"Published Version","publication":"Journal of Structural Biology","date_created":"2021-11-15T12:21:42Z","scopus_import":"1","corr_author":"1","type":"journal_article","article_type":"original","citation":{"chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier, 2021.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>"},"language":[{"iso":"eng"}],"date_updated":"2026-07-06T12:57:43Z","ddc":["572"],"intvolume":"       213","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"author":[{"full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","orcid":"0000-0001-8370-6161","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"publication_status":"published","file_date_updated":"2021-11-15T13:11:27Z","year":"2021","month":"11","related_material":{"record":[{"relation":"software","status":"public","id":"14502"}]},"issue":"4","volume":213,"das_tickbox":"1","article_number":"107808","_id":"10290","date_published":"2021-11-03T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","file":[{"success":1,"checksum":"6b209e4d44775d4e02b50f78982c15fa","date_updated":"2021-11-15T13:11:27Z","file_name":"2021_JournalStructBiol_Dimchev.pdf","file_id":"10291","file_size":16818304,"content_type":"application/pdf","date_created":"2021-11-15T13:11:27Z","relation":"main_file","creator":"cchlebak","access_level":"open_access"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","isi":1,"doi":"10.1016/j.jsb.2021.107808","publication_identifier":{"issn":["1047-8477"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","oa":1,"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FlSc"}],"keyword":["Structural Biology"],"day":"03"},{"month":"04","volume":524,"publication_status":"published","year":"2021","pmid":1,"author":[{"first_name":"Kseniia","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","full_name":"Khudiakova, Kseniia"},{"full_name":"Neretina, Tatiana Yu.","first_name":"Tatiana Yu.","last_name":"Neretina"},{"full_name":"Kondrashov, Alexey S.","first_name":"Alexey S.","last_name":"Kondrashov"}],"date_updated":"2026-07-06T12:58:31Z","intvolume":"       524","citation":{"chicago":"Khudiakova, Kseniia, Tatiana Yu. Neretina, and Alexey S. Kondrashov. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>.","ista":"Khudiakova K, Neretina TY, Kondrashov AS. 2021. Two linked loci under mutation-selection balance and Muller’s ratchet. Journal of Theoretical Biology. 524, 110729.","ama":"Khudiakova K, Neretina TY, Kondrashov AS. Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. 2021;524. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>","ieee":"K. Khudiakova, T. Y. Neretina, and A. S. Kondrashov, “Two linked loci under mutation-selection balance and Muller’s ratchet,” <i>Journal of Theoretical Biology</i>, vol. 524. Elsevier, 2021.","apa":"Khudiakova, K., Neretina, T. Y., &#38; Kondrashov, A. S. (2021). Two linked loci under mutation-selection balance and Muller’s ratchet. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">https://doi.org/10.1016/j.jtbi.2021.110729</a>","short":"K. Khudiakova, T.Y. Neretina, A.S. Kondrashov, Journal of Theoretical Biology 524 (2021).","mla":"Khudiakova, Kseniia, et al. “Two Linked Loci under Mutation-Selection Balance and Muller’s Ratchet.” <i>Journal of Theoretical Biology</i>, vol. 524, 110729, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2021.110729\">10.1016/j.jtbi.2021.110729</a>."},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"text":"We report the complete analysis of a deterministic model of deleterious mutations and negative selection against them at two haploid loci without recombination. As long as mutation is a weaker force than selection, mutant alleles remain rare at the only stable equilibrium, and otherwise, a variety of dynamics are possible. If the mutation-free genotype is absent, generally the only stable equilibrium is the one that corresponds to fixation of the mutant allele at the locus where it is less deleterious. This result suggests that fixation of a deleterious allele that follows a click of the Muller’s ratchet is governed by natural selection, instead of random drift.","lang":"eng"}],"external_id":{"pmid":["33901507"],"isi":["000659161500002"]},"status":"public","date_created":"2021-05-12T05:58:42Z","publication":"Journal of Theoretical Biology","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/477489v1","open_access":"1"}],"type":"journal_article","department":[{"_id":"GradSch"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","Modelling and Simulation","Statistics and Probability","General Immunology and Microbiology","Applied Mathematics","General Agricultural and Biological Sciences","General Medicine"],"day":"24","oa":1,"title":"Two linked loci under mutation-selection balance and Muller’s ratchet","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0022-5193"]},"article_processing_charge":"No","publisher":"Elsevier","doi":"10.1016/j.jtbi.2021.110729","acknowledgement":"This work was supported by the Russian Science Foundation grant N 16-14-10173.","isi":1,"article_number":"110729","quality_controlled":"1","_id":"9387","date_published":"2021-04-24T00:00:00Z","das_tickbox":"1"},{"file":[{"success":1,"checksum":"990bccc527c64d85cf1c97885110b5f4","file_name":"2021_AdvancedMaterials_Liu.pdf","file_id":"10720","date_updated":"2022-02-03T13:16:14Z","file_size":5595666,"content_type":"application/pdf","date_created":"2022-02-03T13:16:14Z","creator":"cchlebak","relation":"main_file","access_level":"open_access"}],"acknowledgement":"Y.L. and M.C. contributed equally to this work. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. M.C. has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. Y.Y. and O.C.-M. acknowledge the financial support from DFG within the project SFB 917: Nanoswitches. J.L. is a Serra Húnter Fellow and is grateful to ICREA Academia program. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N.","doi":"10.1002/adma.202106858","isi":1,"publisher":"Wiley","_id":"10123","date_published":"2021-12-29T00:00:00Z","quality_controlled":"1","article_number":"2106858","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe","oa":1,"day":"29","keyword":["mechanical engineering","mechanics of materials","general materials science"],"department":[{"_id":"EM-Fac"},{"_id":"MaIb"}],"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"intvolume":"        33","ddc":["620"],"date_updated":"2026-07-06T13:07:38Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"type":"journal_article","corr_author":"1","scopus_import":"1","publication":"Advanced Materials","date_created":"2021-10-11T20:07:24Z","oa_version":"Published Version","status":"public","external_id":{"pmid":["34626034"],"isi":["000709899300001"]},"has_accepted_license":"1","abstract":[{"text":"Solution synthesis of particles emerged as an alternative to prepare thermoelectric materials with less demanding processing conditions than conventional solid-state synthetic methods. However, solution synthesis generally involves the presence of additional molecules or ions belonging to the precursors or added to enable solubility and/or regulate nucleation and growth. These molecules or ions can end up in the particles as surface adsorbates and interfere in the material properties. This work demonstrates that ionic adsorbates, in particular Na⁺ ions, are electrostatically adsorbed in SnSe particles synthesized in water and play a crucial role not only in directing the material nano/microstructure but also in determining the transport properties of the consolidated material. In dense pellets prepared by sintering SnSe particles, Na remains within the crystal lattice as dopant, in dislocations, precipitates, and forming grain boundary complexions. These results highlight the importance of considering all the possible unintentional impurities to establish proper structure-property relationships and control material properties in solution-processed thermoelectric materials.","lang":"eng"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Liu, Yu, Mariano Calcabrini, Yuan Yu, Aziz Genç, Cheng Chang, Tommaso Costanzo, Tobias Kleinhanns, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>.","short":"Y. Liu, M. Calcabrini, Y. Yu, A. Genç, C. Chang, T. Costanzo, T. Kleinhanns, S. Lee, J. Llorca, O. Cojocaru‐Mirédin, M. Ibáñez, Advanced Materials 33 (2021).","mla":"Liu, Yu, et al. “The Importance of Surface Adsorbates in Solution‐processed Thermoelectric Materials: The Case of SnSe.” <i>Advanced Materials</i>, vol. 33, no. 52, 2106858, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>.","ama":"Liu Y, Calcabrini M, Yu Y, et al. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. 2021;33(52). doi:<a href=\"https://doi.org/10.1002/adma.202106858\">10.1002/adma.202106858</a>","ieee":"Y. Liu <i>et al.</i>, “The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe,” <i>Advanced Materials</i>, vol. 33, no. 52. Wiley, 2021.","ista":"Liu Y, Calcabrini M, Yu Y, Genç A, Chang C, Costanzo T, Kleinhanns T, Lee S, Llorca J, Cojocaru‐Mirédin O, Ibáñez M. 2021. The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. Advanced Materials. 33(52), 2106858.","apa":"Liu, Y., Calcabrini, M., Yu, Y., Genç, A., Chang, C., Costanzo, T., … Ibáñez, M. (2021). The importance of surface adsorbates in solution‐processed thermoelectric materials: The case of SnSe. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106858\">https://doi.org/10.1002/adma.202106858</a>"},"ec_funded":1,"year":"2021","publication_status":"published","file_date_updated":"2022-02-03T13:16:14Z","volume":33,"related_material":{"record":[{"relation":"dissertation_contains","id":"12885","status":"public"},{"relation":"later_version","id":"17062","status":"public"}]},"issue":"52","month":"12","author":[{"last_name":"Liu","first_name":"Yu","orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano","last_name":"Calcabrini","first_name":"Mariano","orcid":"0000-0003-4566-5877"},{"first_name":"Yuan","last_name":"Yu","full_name":"Yu, Yuan"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"last_name":"Chang","orcid":"0000-0002-9515-4277","first_name":"Cheng","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"last_name":"Kleinhanns","orcid":"0000-0003-1537-7436","first_name":"Tobias","full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425"},{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Cojocaru‐Mirédin, Oana","last_name":"Cojocaru‐Mirédin","first_name":"Oana"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"pmid":1},{"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"intvolume":"      2218","date_updated":"2026-07-06T13:11:10Z","language":[{"iso":"eng"}],"citation":{"short":"P. Xia, C.-P.J. Heisenberg, in:, R. Dosch (Ed.), Germline Development in the Zebrafish, Humana Press, 2021, pp. 117–128.","mla":"Xia, Peng, and Carl-Philipp J. Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, vol. 2218, Humana Press, 2021, pp. 117–28, doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>.","ista":"Xia P, Heisenberg C-PJ. 2021.Quantifying tissue tension in the granulosa layer after laser surgery. In: Germline Development in the Zebrafish. Methods in Molecular Biology, vol. 2218, 117–128.","ama":"Xia P, Heisenberg C-PJ. Quantifying tissue tension in the granulosa layer after laser surgery. In: Dosch R, ed. <i>Germline Development in the Zebrafish</i>. Vol 2218. Humana Press; 2021:117-128. doi:<a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">10.1007/978-1-0716-0970-5_10</a>","ieee":"P. Xia and C.-P. J. Heisenberg, “Quantifying tissue tension in the granulosa layer after laser surgery,” in <i>Germline Development in the Zebrafish</i>, vol. 2218, R. Dosch, Ed. Humana Press, 2021, pp. 117–128.","apa":"Xia, P., &#38; Heisenberg, C.-P. J. (2021). Quantifying tissue tension in the granulosa layer after laser surgery. In R. Dosch (Ed.), <i>Germline Development in the Zebrafish</i> (Vol. 2218, pp. 117–128). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>","chicago":"Xia, Peng, and Carl-Philipp J Heisenberg. “Quantifying Tissue Tension in the Granulosa Layer after Laser Surgery.” In <i>Germline Development in the Zebrafish</i>, edited by Roland Dosch, 2218:117–28. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-0970-5_10\">https://doi.org/10.1007/978-1-0716-0970-5_10</a>."},"ec_funded":1,"type":"book_chapter","corr_author":"1","publication":"Germline Development in the Zebrafish","date_created":"2021-03-14T23:01:34Z","scopus_import":"1","oa_version":"None","external_id":{"pmid":["33606227"]},"status":"public","abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data."}],"volume":2218,"month":"02","year":"2021","publication_status":"published","pmid":1,"page":"117-128","alternative_title":["Methods in Molecular Biology"],"author":[{"orcid":"0000-0002-5419-7756","first_name":"Peng","last_name":"Xia","full_name":"Xia, Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.1007/978-1-0716-0970-5_10","acknowledgement":"We thank Prof. Masazumi Tada and Roland Dosch for providing transgenic zebrafish lines, the Heisenberg lab for technical assistance and feedback on the manuscript, and the Bioimaging and Fish facilities of IST Austria for continuous support. This work was funded by an ERC advanced grant (MECSPEC to C.-P.H.).","publisher":"Humana Press","_id":"9245","quality_controlled":"1","date_published":"2021-02-20T00:00:00Z","das_tickbox":"1","editor":[{"full_name":"Dosch, Roland","last_name":"Dosch","first_name":"Roland"}],"day":"20","keyword":["Tissue tension","Morphogenesis","Laser ablation","Zebrafish folliculogenesis","Granulosa cells"],"department":[{"_id":"CaHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quantifying tissue tension in the granulosa layer after laser surgery","article_processing_charge":"No","publication_identifier":{"eisbn":["978-1-0716-0970-5"],"issn":["1064-3745"],"isbn":["978-1-0716-0969-9"],"eissn":["1940-6029"]}},{"status":"public","corr_author":"1","type":"conference_abstract","main_file_link":[{"url":"https://doi.org/10.29363/nanoge.incnc.2021.050","open_access":"1"}],"date_created":"2024-04-03T08:28:26Z","oa_version":"Published Version","publication":"Proceedings of the Internet NanoGe Conference on Nanocrystals","language":[{"iso":"eng"}],"article_number":"050","citation":{"chicago":"Balazs, Daniel, Jessica Cimada da Silva, Tyler Dunbar, Maria Ibáñez, and Tobias Hanrath. “Controlled Reactive Assembly of Colloidal Nanocrystal Superlattices: Mechanism and Kinetics.” In <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Fundació de la comunitat valenciana SCITO, 2021. <a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">https://doi.org/10.29363/nanoge.incnc.2021.050</a>.","apa":"Balazs, D., Cimada da Silva, J., Dunbar, T., Ibáñez, M., &#38; Hanrath, T. (2021). Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. In <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Virtual: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">https://doi.org/10.29363/nanoge.incnc.2021.050</a>","ista":"Balazs D, Cimada da Silva J, Dunbar T, Ibáñez M, Hanrath T. 2021. Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. Proceedings of the Internet NanoGe Conference on Nanocrystals. iNCNC: Internet nanoGe Conference on Nanocrystals, 050.","ieee":"D. Balazs, J. Cimada da Silva, T. Dunbar, M. Ibáñez, and T. Hanrath, “Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics,” in <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>, Virtual, 2021.","ama":"Balazs D, Cimada da Silva J, Dunbar T, Ibáñez M, Hanrath T. Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics. In: <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>. Fundació de la comunitat valenciana SCITO; 2021. doi:<a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">10.29363/nanoge.incnc.2021.050</a>","mla":"Balazs, Daniel, et al. “Controlled Reactive Assembly of Colloidal Nanocrystal Superlattices: Mechanism and Kinetics.” <i>Proceedings of the Internet NanoGe Conference on Nanocrystals</i>, 050, Fundació de la comunitat valenciana SCITO, 2021, doi:<a href=\"https://doi.org/10.29363/nanoge.incnc.2021.050\">10.29363/nanoge.incnc.2021.050</a>.","short":"D. Balazs, J. Cimada da Silva, T. Dunbar, M. Ibáñez, T. Hanrath, in:, Proceedings of the Internet NanoGe Conference on Nanocrystals, Fundació de la comunitat valenciana SCITO, 2021."},"quality_controlled":"1","_id":"15280","date_published":"2021-06-08T00:00:00Z","ddc":["530"],"conference":{"end_date":"2021-07-02","start_date":"2021-06-28","location":"Virtual","name":"iNCNC: Internet nanoGe Conference on Nanocrystals"},"date_updated":"2026-07-06T13:07:52Z","publisher":"Fundació de la comunitat valenciana SCITO","doi":"10.29363/nanoge.incnc.2021.050","author":[{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","orcid":"0000-0001-7597-043X","first_name":"Daniel"},{"full_name":"Cimada da Silva, Jessica","first_name":"Jessica","last_name":"Cimada da Silva"},{"full_name":"Dunbar, Tyler","last_name":"Dunbar","first_name":"Tyler"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Tobias","last_name":"Hanrath","full_name":"Hanrath, Tobias"}],"article_processing_charge":"No","title":"Controlled reactive assembly of colloidal nanocrystal superlattices: Mechanism and kinetics","publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","month":"06","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"day":"08"}]