[{"external_id":{"pmid":["37390457"],"isi":["001020623900001"]},"author":[{"orcid":"0000-0001-6928-074X","first_name":"Rhys","last_name":"Bunting","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","full_name":"Bunting, Rhys"},{"id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","full_name":"Wodaczek, Felix","last_name":"Wodaczek","first_name":"Felix","orcid":"0009-0000-1457-795X"},{"full_name":"Torabi, Tina","last_name":"Torabi","first_name":"Tina"},{"orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"}],"title":"Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"MaIb"},{"_id":"BiCh"}],"file":[{"file_size":3155843,"content_type":"application/pdf","date_created":"2023-07-12T10:22:04Z","access_level":"open_access","date_updated":"2023-07-12T10:22:04Z","relation":"main_file","checksum":"e07d5323f9c0e5cbd1ad6453f29440ab","creator":"cchlebak","file_id":"13219","file_name":"2023_JACS_Bunting.pdf","success":1}],"scopus_import":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1","oa_version":"Published Version","day":"30","ddc":["540"],"abstract":[{"lang":"eng","text":"Physical catalysts often have multiple sites where reactions can take place. One prominent example is single-atom alloys, where the reactive dopant atoms can preferentially locate in the bulk or at different sites on the surface of the nanoparticle. However, ab initio modeling of catalysts usually only considers one site of the catalyst, neglecting the effects of multiple sites. Here, nanoparticles of copper doped with single-atom rhodium or palladium are modeled for the dehydrogenation of propane. Single-atom alloy nanoparticles are simulated at 400–600 K, using machine learning potentials trained on density functional theory calculations, and then the occupation of different single-atom active sites is identified using a similarity kernel. Further, the turnover frequency for all possible sites is calculated for propane dehydrogenation to propene through microkinetic modeling using density functional theory calculations. The total turnover frequencies of the whole nanoparticle are then described from both the population and the individual turnover frequency of each site. Under operating conditions, rhodium as a dopant is found to almost exclusively occupy (111) surface sites while palladium as a dopant occupies a greater variety of facets. Undercoordinated dopant surface sites are found to tend to be more reactive for propane dehydrogenation compared to the (111) surface. It is found that considering the dynamics of the single-atom alloy nanoparticle has a profound effect on the calculated catalytic activity of single-atom alloys by several orders of magnitude."}],"issue":"27","publication":"Journal of the American Chemical Society","date_created":"2023-07-12T09:16:40Z","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2023-06-30T00:00:00Z","file_date_updated":"2023-07-12T10:22:04Z","citation":{"ista":"Bunting R, Wodaczek F, Torabi T, Cheng B. 2023. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. Journal of the American Chemical Society. 145(27), 14894–14902.","short":"R. Bunting, F. Wodaczek, T. Torabi, B. Cheng, Journal of the American Chemical Society 145 (2023) 14894–14902.","apa":"Bunting, R., Wodaczek, F., Torabi, T., &#38; Cheng, B. (2023). Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>","mla":"Bunting, Rhys, et al. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27, American Chemical Society, 2023, pp. 14894–902, doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>.","ieee":"R. Bunting, F. Wodaczek, T. Torabi, and B. Cheng, “Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 27. American Chemical Society, pp. 14894–14902, 2023.","ama":"Bunting R, Wodaczek F, Torabi T, Cheng B. Reactivity of single-atom alloy nanoparticles: Modeling the dehydrogenation of propane. <i>Journal of the American Chemical Society</i>. 2023;145(27):14894-14902. doi:<a href=\"https://doi.org/10.1021/jacs.3c04030\">10.1021/jacs.3c04030</a>","chicago":"Bunting, Rhys, Felix Wodaczek, Tina Torabi, and Bingqing Cheng. “Reactivity of Single-Atom Alloy Nanoparticles: Modeling the Dehydrogenation of Propane.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c04030\">https://doi.org/10.1021/jacs.3c04030</a>."},"article_processing_charge":"Yes (via OA deal)","month":"06","volume":145,"oa":1,"intvolume":"       145","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","type":"journal_article","publisher":"American Chemical Society","date_updated":"2024-10-21T06:01:30Z","acknowledgement":"B.C. acknowledges resources provided by the Cambridge Tier2 system operated by the University of Cambridge Research\r\nComputing Service funded by EPSRC Tier-2 capital grant EP/\r\nP020259/1.","doi":"10.1021/jacs.3c04030","pmid":1,"year":"2023","page":"14894-14902","_id":"13216","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","isi":1},{"author":[{"orcid":"0000-0002-1071-6091","last_name":"Benedikter","first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","full_name":"Benedikter, Niels P"},{"full_name":"Porta, Marcello","first_name":"Marcello","last_name":"Porta"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"external_id":{"arxiv":["2106.13185"],"isi":["001024369000001"]},"department":[{"_id":"RoSe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_size":851626,"content_type":"application/pdf","file_name":"2023_ArchiveRationalMechAnalysis_Benedikter.pdf","success":1,"date_created":"2023-11-14T13:12:12Z","access_level":"open_access","date_updated":"2023-11-14T13:12:12Z","relation":"main_file","creator":"dernst","checksum":"2b45828d854a253b14bf7aa196ec55e9","file_id":"14535"}],"title":"Correlation energy of a weakly interacting Fermi gas with large interaction potential","has_accepted_license":"1","article_number":"65","scopus_import":"1","publication_status":"published","day":"01","ddc":["510"],"abstract":[{"text":"Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.","lang":"eng"}],"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"publication":"Archive for Rational Mechanics and Analysis","issue":"4","oa_version":"Published Version","ec_funded":1,"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"date_created":"2023-07-16T22:01:08Z","citation":{"ama":"Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas with large interaction potential. <i>Archive for Rational Mechanics and Analysis</i>. 2023;247(4). doi:<a href=\"https://doi.org/10.1007/s00205-023-01893-6\">10.1007/s00205-023-01893-6</a>","chicago":"Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00205-023-01893-6\">https://doi.org/10.1007/s00205-023-01893-6</a>.","apa":"Benedikter, N. P., Porta, M., Schlein, B., &#38; Seiringer, R. (2023). Correlation energy of a weakly interacting Fermi gas with large interaction potential. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-023-01893-6\">https://doi.org/10.1007/s00205-023-01893-6</a>","ieee":"N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas with large interaction potential,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 4. Springer Nature, 2023.","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 4, 65, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00205-023-01893-6\">10.1007/s00205-023-01893-6</a>.","ista":"Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 247(4), 65.","short":"N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational Mechanics and Analysis 247 (2023)."},"oa":1,"article_processing_charge":"Yes (via OA deal)","volume":247,"month":"08","date_published":"2023-08-01T00:00:00Z","file_date_updated":"2023-11-14T13:12:12Z","doi":"10.1007/s00205-023-01893-6","acknowledgement":"RS was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). MP acknowledges financial support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement.","intvolume":"       247","date_updated":"2025-04-14T07:26:58Z","status":"public","publisher":"Springer Nature","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","year":"2023","_id":"13225"},{"acknowledgement":"It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee for many constructive comments. L.B. gratefully acknowledges funding from the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen Access funding enabled and organized by Projekt DEAL.","doi":"10.1007/s11005-023-01698-4","intvolume":"       113","publisher":"Springer Nature","status":"public","type":"journal_article","date_updated":"2025-06-25T06:20:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"hybrid","article_type":"original","isi":1,"year":"2023","_id":"13226","quality_controlled":"1","publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:08Z","arxiv":1,"citation":{"ista":"Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 113(4), 77.","short":"L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023).","apa":"Bossmann, L., &#38; Petrat, S. P. (2023). Weak Edgeworth expansion for the mean-field Bose gas. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-023-01698-4\">https://doi.org/10.1007/s11005-023-01698-4</a>","mla":"Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” <i>Letters in Mathematical Physics</i>, vol. 113, no. 4, 77, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s11005-023-01698-4\">10.1007/s11005-023-01698-4</a>.","ieee":"L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field Bose gas,” <i>Letters in Mathematical Physics</i>, vol. 113, no. 4. Springer Nature, 2023.","chicago":"Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11005-023-01698-4\">https://doi.org/10.1007/s11005-023-01698-4</a>.","ama":"Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas. <i>Letters in Mathematical Physics</i>. 2023;113(4). doi:<a href=\"https://doi.org/10.1007/s11005-023-01698-4\">10.1007/s11005-023-01698-4</a>"},"month":"07","article_processing_charge":"Yes (via OA deal)","volume":113,"oa":1,"date_published":"2023-07-03T00:00:00Z","file_date_updated":"2025-06-25T06:20:02Z","OA_place":"publisher","has_accepted_license":"1","article_number":"77","scopus_import":"1","publication_status":"published","corr_author":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"day":"03","ddc":["510"],"abstract":[{"lang":"eng","text":"We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion."}],"publication":"Letters in Mathematical Physics","issue":"4","oa_version":"Published Version","ec_funded":1,"author":[{"orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","full_name":"Bossmann, Lea","last_name":"Bossmann","first_name":"Lea"},{"last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889"}],"external_id":{"arxiv":["2208.00199"],"isi":["001022878900002"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"RoSe"}],"file":[{"success":1,"file_name":"2023_LettersMathPhysics_Bossmann.pdf","checksum":"995c902a989a6769fd3db456cfd41111","creator":"dernst","file_id":"19898","access_level":"open_access","relation":"main_file","date_updated":"2025-06-25T06:20:02Z","date_created":"2025-06-25T06:20:02Z","content_type":"application/pdf","file_size":586698}],"title":"Weak Edgeworth expansion for the mean-field Bose gas"},{"date_updated":"2026-01-21T07:23:43Z","publisher":"Association for Computing Machinery","status":"public","type":"conference","doi":"10.1145/3593013.3594028","acknowledgement":"The authors would like to thank the anonymous reviewers for their valuable comments and helpful suggestions. This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","_id":"13228","page":"604-614","year":"2023","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_created":"2023-07-16T22:01:09Z","conference":{"location":"Chicago, IL, United States","start_date":"2023-06-12","end_date":"2023-06-15","name":"FAccT: Conference on Fairness, Accountability and Transparency"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450372527"]},"quality_controlled":"1","file_date_updated":"2023-07-18T07:43:10Z","date_published":"2023-06-12T00:00:00Z","oa":1,"article_processing_charge":"Yes (via OA deal)","month":"06","citation":{"chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Runtime Monitoring of Dynamic Fairness Properties.” In <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, 604–14. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3593013.3594028\">https://doi.org/10.1145/3593013.3594028</a>.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic fairness properties. In: <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>. Association for Computing Machinery; 2023:604-614. doi:<a href=\"https://doi.org/10.1145/3593013.3594028\">10.1145/3593013.3594028</a>","mla":"Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.” <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, Association for Computing Machinery, 2023, pp. 604–14, doi:<a href=\"https://doi.org/10.1145/3593013.3594028\">10.1145/3593013.3594028</a>.","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring of dynamic fairness properties,” in <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i>, Chicago, IL, United States, 2023, pp. 604–614.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., &#38; Mallik, K. (2023). Runtime monitoring of dynamic fairness properties. In <i>FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency</i> (pp. 604–614). Chicago, IL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3593013.3594028\">https://doi.org/10.1145/3593013.3594028</a>","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–614.","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness, Accountability and Transparency, 604–614."},"publication_status":"published","corr_author":"1","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"oa_version":"Published Version","publication":"FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency","abstract":[{"lang":"eng","text":"A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox."}],"day":"12","ddc":["000"],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"external_id":{"isi":["001062819300057"],"arxiv":["2305.04699"]},"author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"last_name":"Karimi","first_name":"Mahyar","id":"6e5417ba-5355-11ee-ae5a-94c2e510b26b","full_name":"Karimi, Mahyar","orcid":"0009-0005-0820-1696"},{"orcid":"0000-0001-8974-2542","full_name":"Kueffner, Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin","last_name":"Kueffner"},{"last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475"}],"title":"Runtime monitoring of dynamic fairness properties","file":[{"checksum":"96c759db9cdf94b81e37871a66a6ff48","file_id":"13245","creator":"dernst","relation":"main_file","date_updated":"2023-07-18T07:43:10Z","access_level":"open_access","date_created":"2023-07-18T07:43:10Z","success":1,"file_name":"2023_ACM_HenzingerT.pdf","content_type":"application/pdf","file_size":4100596}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"ToHe"}]},{"ec_funded":1,"oa_version":"Published Version","issue":"6","publication":"PLoS Biology","ddc":["570"],"day":"08","abstract":[{"lang":"eng","text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation."}],"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","publication_status":"published","scopus_import":"1","has_accepted_license":"1","title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","file":[{"content_type":"application/pdf","file_size":4431723,"checksum":"8e88cb0e5a6433a2f1939a9030bed384","file_id":"13246","creator":"dernst","access_level":"open_access","date_updated":"2023-07-18T07:59:58Z","relation":"main_file","date_created":"2023-07-18T07:59:58Z","file_name":"2023_PloSBiology_Shamipour.pdf","success":1}],"department":[{"_id":"CaHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001003199100005"],"pmid":["37289834"]},"author":[{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"full_name":"Hofmann, Laura","last_name":"Hofmann","first_name":"Laura","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","full_name":"Steccari, Irene","last_name":"Steccari"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos","full_name":"Kardos, Roland","first_name":"Roland"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"_id":"13229","page":"e3002146","pmid":1,"year":"2023","isi":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-14T07:46:59Z","status":"public","type":"journal_article","publisher":"Public Library of Science","intvolume":"        21","doi":"10.1371/journal.pbio.3002146","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","file_date_updated":"2023-07-18T07:59:58Z","date_published":"2023-06-08T00:00:00Z","oa":1,"month":"06","volume":21,"article_processing_charge":"No","citation":{"ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. 2023;21(6):e3002146. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>.","ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” <i>PLoS Biology</i>, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., &#38; Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146."},"date_created":"2023-07-16T22:01:09Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1545-7885"]}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"original","pmid":1,"year":"2023","_id":"13230","doi":"10.1371/journal.pcbi.1011104","acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","intvolume":"        19","date_updated":"2023-08-02T06:33:50Z","publisher":"Public Library of Science","type":"journal_article","status":"public","citation":{"mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>.","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” <i>PLoS Computational Biology</i>, vol. 19, no. 6. Public Library of Science, 2023.","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., &#38; Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>.","short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104."},"oa":1,"month":"06","article_processing_charge":"No","volume":19,"date_published":"2023-06-08T00:00:00Z","file_date_updated":"2023-07-18T08:07:59Z","quality_controlled":"1","publication_identifier":{"eissn":["1553-7358"]},"language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:09Z","abstract":[{"text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.","lang":"eng"}],"ddc":["570"],"day":"08","issue":"6","publication":"PLoS Computational Biology","oa_version":"Published Version","has_accepted_license":"1","article_number":"e1011104","scopus_import":"1","publication_status":"published","department":[{"_id":"MaJö"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","file_size":2281868,"file_name":"2023_PloSCompBio_Charlton.pdf","success":1,"checksum":"800761fa2c647fabd6ad034589bc526e","file_id":"13247","creator":"dernst","relation":"main_file","date_updated":"2023-07-18T08:07:59Z","access_level":"open_access","date_created":"2023-07-18T08:07:59Z"}],"title":"Environmental dynamics shape perceptual decision bias","author":[{"first_name":"Julie A.","last_name":"Charlton","full_name":"Charlton, Julie A."},{"first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski"},{"full_name":"Bai, Yoon H.","first_name":"Yoon H.","last_name":"Bai"},{"first_name":"Ann M.","full_name":"Hermundstad, Ann M.","last_name":"Hermundstad"},{"full_name":"Goris, Robbe L.T.","last_name":"Goris","first_name":"Robbe L.T."}],"external_id":{"isi":["001003410200003"],"pmid":["37289753"]}},{"acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","doi":"10.1103/PhysRevE.107.065207","date_updated":"2025-03-06T14:02:33Z","status":"public","type":"journal_article","publisher":"American Physical Society","intvolume":"       107","isi":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13231","year":"2023","pmid":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"arxiv":1,"date_created":"2023-07-16T22:01:10Z","oa":1,"article_processing_charge":"No","volume":107,"month":"06","citation":{"chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., &#38; Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">https://doi.org/10.1103/PhysRevE.107.065207</a>","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” <i>Physical Review E</i>, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.065207\">10.1103/PhysRevE.107.065207</a>.","ieee":"M. Schörner <i>et al.</i>, “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” <i>Physical Review E</i>, vol. 107, no. 6. American Physical Society, 2023.","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023)."},"date_published":"2023-06-14T00:00:00Z","article_number":"065207","publication_status":"published","scopus_import":"1","issue":"6","publication":"Physical Review E","day":"14","abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"oa_version":"Preprint","author":[{"full_name":"Schörner, Maximilian","first_name":"Maximilian","last_name":"Schörner"},{"full_name":"Bethkenhagen, Mandy","first_name":"Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129"},{"last_name":"Döppner","full_name":"Döppner, Tilo","first_name":"Tilo"},{"first_name":"Dominik","full_name":"Kraus, Dominik","last_name":"Kraus"},{"last_name":"Fletcher","full_name":"Fletcher, Luke B.","first_name":"Luke B."},{"first_name":"Siegfried H.","full_name":"Glenzer, Siegfried H.","last_name":"Glenzer"},{"full_name":"Redmer, Ronald","first_name":"Ronald","last_name":"Redmer"}],"external_id":{"isi":["001020265000002"],"arxiv":["2301.01545"],"pmid":["37464593"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"department":[{"_id":"BiCh"}],"title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula"},{"citation":{"short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>, vol. 11, no. 6, 1014, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” <i>Vaccines</i>, vol. 11, no. 6. MDPI, 2023.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. MDPI. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. 2023;11(6). doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>."},"month":"06","article_processing_charge":"No","volume":11,"oa":1,"date_published":"2023-06-01T00:00:00Z","file_date_updated":"2023-07-18T07:25:43Z","quality_controlled":"1","publication_identifier":{"eissn":["2076-393X"]},"language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"year":"2023","pmid":1,"_id":"13232","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","doi":"10.3390/vaccines11061014","intvolume":"        11","status":"public","publisher":"MDPI","type":"journal_article","date_updated":"2025-04-23T13:01:23Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"LeSa"}],"file":[{"success":1,"file_name":"2023_Vaccines_Dormeshkin.pdf","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","file_id":"13244","creator":"dernst","date_updated":"2023-07-18T07:25:43Z","relation":"main_file","access_level":"open_access","date_created":"2023-07-18T07:25:43Z","content_type":"application/pdf","file_size":2339746}],"title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"last_name":"Katsin","first_name":"Mikalai","full_name":"Katsin, Mikalai"},{"full_name":"Stegantseva, Maria","last_name":"Stegantseva","first_name":"Maria"},{"last_name":"Golenchenko","full_name":"Golenchenko, Sergey","first_name":"Sergey"},{"last_name":"Shapira","full_name":"Shapira, Michail","first_name":"Michail"},{"first_name":"Simon","full_name":"Dubovik, Simon","last_name":"Dubovik"},{"full_name":"Lutskovich, Dzmitry","first_name":"Dzmitry","last_name":"Lutskovich"},{"id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton","first_name":"Anton","last_name":"Kavaleuski","orcid":"0000-0003-2091-526X"},{"first_name":"Alexander","full_name":"Meleshko, Alexander","last_name":"Meleshko"}],"external_id":{"pmid":["37376403"],"isi":["001017740000001"]},"abstract":[{"text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.","lang":"eng"}],"day":"01","ddc":["570"],"issue":"6","publication":"Vaccines","oa_version":"Published Version","has_accepted_license":"1","article_number":"1014","scopus_import":"1","publication_status":"published"},{"publication_status":"published","corr_author":"1","scopus_import":"1","article_number":"L061304","ec_funded":1,"oa_version":"Preprint","issue":"6","publication":"Physical Review A","abstract":[{"text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.","lang":"eng"}],"day":"20","project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2302.01022"],"isi":["001019748000005"]},"author":[{"full_name":"Agafonova, Sofya","last_name":"Agafonova","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","first_name":"Sofya","orcid":"0000-0003-0582-2946"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"}],"title":"Finite-range bias in fitting three-body loss to the zero-range model","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.01022","open_access":"1"}],"department":[{"_id":"MiLe"},{"_id":"OnHo"}],"date_updated":"2025-04-14T07:48:53Z","publisher":"American Physical Society","type":"journal_article","status":"public","intvolume":"       107","doi":"10.1103/PhysRevA.107.L061304","acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","_id":"13233","year":"2023","isi":1,"article_type":"letter_note","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"date_created":"2023-07-16T22:01:10Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"date_published":"2023-06-20T00:00:00Z","oa":1,"article_processing_charge":"No","month":"06","volume":107,"citation":{"short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>.","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>","mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” <i>Physical Review A</i>, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">10.1103/PhysRevA.107.L061304</a>.","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","apa":"Agafonova, S., Lemeshko, M., &#38; Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.L061304\">https://doi.org/10.1103/PhysRevA.107.L061304</a>"}},{"file":[{"file_size":13387667,"content_type":"application/pdf","success":1,"file_name":"2023_JourSoftwareTools_Kueffner.pdf","relation":"main_file","access_level":"open_access","date_updated":"2024-01-30T12:06:07Z","date_created":"2024-01-30T12:06:07Z","file_id":"14903","creator":"dernst","checksum":"3c4b347f39412a76872f9a6f30101f94"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"ToHe"}],"title":"Into the unknown: Active monitoring of neural networks (extended version)","author":[{"id":"8121a2d0-dc85-11ea-9058-af578f3b4515","full_name":"Kueffner, Konstantin","first_name":"Konstantin","last_name":"Kueffner","orcid":"0000-0001-8974-2542"},{"first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","full_name":"Lukina, Anna","last_name":"Lukina"},{"orcid":"0000-0003-3658-1065","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Schilling, Christian"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"external_id":{"arxiv":["2009.06429"],"isi":["001020160000001"]},"publication":"International Journal on Software Tools for Technology Transfer","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"ddc":["000"],"abstract":[{"lang":"eng","text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure."}],"day":"01","ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"id":"10206","relation":"shorter_version","status":"public"}]},"has_accepted_license":"1","corr_author":"1","publication_status":"published","scopus_import":"1","month":"08","volume":25,"article_processing_charge":"Yes (in subscription journal)","oa":1,"citation":{"chicago":"Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>.","ama":"Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. 2023;25:575-592. doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>","mla":"Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25, Springer Nature, 2023, pp. 575–92, doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>.","ieee":"K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: Active monitoring of neural networks (extended version),” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25. Springer Nature, pp. 575–592, 2023.","apa":"Kueffner, K., Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2023). Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>","short":"K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 25 (2023) 575–592.","ista":"Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. 25, 575–592."},"file_date_updated":"2024-01-30T12:06:07Z","date_published":"2023-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"quality_controlled":"1","date_created":"2023-07-16T22:01:11Z","arxiv":1,"article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"575-592","_id":"13234","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, by DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.","doi":"10.1007/s10009-023-00711-4","publisher":"Springer Nature","status":"public","type":"journal_article","date_updated":"2025-04-15T06:55:00Z","intvolume":"        25"},{"department":[{"_id":"MaIb"}],"title":"Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance","author":[{"full_name":"Liu, Yu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","last_name":"Liu","orcid":"0000-0001-7313-6740"},{"full_name":"Li, Mingquan","first_name":"Mingquan","last_name":"Li"},{"last_name":"Wan","full_name":"Wan, Shanhong","first_name":"Shanhong"},{"full_name":"Lim, Khak Ho","first_name":"Khak Ho","last_name":"Lim"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hong","full_name":"Hong, Min","first_name":"Min"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"external_id":{"pmid":["37310395"],"isi":["001008564800001"]},"day":"13","abstract":[{"lang":"eng","text":"AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications."}],"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"issue":"12","publication":"ACS Nano","oa_version":"None","scopus_import":"1","publication_status":"published","citation":{"chicago":"Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsnano.3c03541\">https://doi.org/10.1021/acsnano.3c03541</a>.","ama":"Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. <i>ACS Nano</i>. 2023;17(12):11923–11934. doi:<a href=\"https://doi.org/10.1021/acsnano.3c03541\">10.1021/acsnano.3c03541</a>","mla":"Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:<a href=\"https://doi.org/10.1021/acsnano.3c03541\">10.1021/acsnano.3c03541</a>.","ieee":"Y. Liu <i>et al.</i>, “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” <i>ACS Nano</i>, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.","apa":"Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c03541\">https://doi.org/10.1021/acsnano.3c03541</a>","short":"Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934.","ista":"Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934."},"article_processing_charge":"No","volume":17,"month":"06","date_published":"2023-06-13T00:00:00Z","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:11Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"original","year":"2023","pmid":1,"_id":"13235","page":"11923–11934","acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","doi":"10.1021/acsnano.3c03541","intvolume":"        17","date_updated":"2025-04-15T06:36:40Z","type":"journal_article","status":"public","publisher":"American Chemical Society"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2023","_id":"13236","page":"453-465","doi":"10.1007/978-3-031-32726-1_32","acknowledgement":"The first author thanks to Chandra Chekuri for useful discussions about this paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","intvolume":"     13904","date_updated":"2025-09-09T12:39:59Z","status":"public","type":"conference","publisher":"Springer Nature","citation":{"ista":"Zheng DW, Henzinger M. 2023. Multiplicative auction algorithm for approximate maximum weight bipartite matching. International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 13904, 453–465.","short":"D.W. Zheng, M. Henzinger, in:, International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2023, pp. 453–465.","ama":"Zheng DW, Henzinger M. Multiplicative auction algorithm for approximate maximum weight bipartite matching. In: <i>International Conference on Integer Programming and Combinatorial Optimization</i>. Vol 13904. Springer Nature; 2023:453-465. doi:<a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">10.1007/978-3-031-32726-1_32</a>","chicago":"Zheng, Da Wei, and Monika Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” In <i>International Conference on Integer Programming and Combinatorial Optimization</i>, 13904:453–65. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">https://doi.org/10.1007/978-3-031-32726-1_32</a>.","apa":"Zheng, D. W., &#38; Henzinger, M. (2023). Multiplicative auction algorithm for approximate maximum weight bipartite matching. In <i>International Conference on Integer Programming and Combinatorial Optimization</i> (Vol. 13904, pp. 453–465). Madison, WI, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">https://doi.org/10.1007/978-3-031-32726-1_32</a>","ieee":"D. W. Zheng and M. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” in <i>International Conference on Integer Programming and Combinatorial Optimization</i>, Madison, WI, United States, 2023, vol. 13904, pp. 453–465.","mla":"Zheng, Da Wei, and Monika Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” <i>International Conference on Integer Programming and Combinatorial Optimization</i>, vol. 13904, Springer Nature, 2023, pp. 453–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-32726-1_32\">10.1007/978-3-031-32726-1_32</a>."},"oa":1,"volume":13904,"article_processing_charge":"No","month":"05","date_published":"2023-05-22T00:00:00Z","quality_controlled":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031327254"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"name":"IPCO: Integer Programming and Combinatorial Optimization","end_date":"2023-06-23","location":"Madison, WI, United States","start_date":"2023-06-21"},"arxiv":1,"date_created":"2023-07-16T22:01:11Z","abstract":[{"text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.","lang":"eng"}],"day":"22","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"publication":"International Conference on Integer Programming and Combinatorial Optimization","oa_version":"Preprint","ec_funded":1,"related_material":{"record":[{"id":"15121","relation":"later_version","status":"public"}]},"alternative_title":["LNCS"],"scopus_import":"1","publication_status":"published","department":[{"_id":"MoHe"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.09217"}],"title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","author":[{"first_name":"Da Wei","full_name":"Zheng, Da Wei","last_name":"Zheng"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"}],"external_id":{"isi":["001281059600032"],"arxiv":["2301.09217"]}},{"publication":"Nature Reviews Physics","abstract":[{"lang":"eng","text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases."}],"day":"01","oa_version":"None","publication_status":"published","scopus_import":"1","department":[{"_id":"AnSa"}],"title":"Amyloid formation as a protein phase transition","author":[{"first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T.","last_name":"Michaels"},{"first_name":"Daoyuan","last_name":"Qian","full_name":"Qian, Daoyuan"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"first_name":"Sara","full_name":"Linse, Sara","last_name":"Linse"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"external_id":{"isi":["001017539800001"]},"article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"379–397","_id":"13237","year":"2023","doi":"10.1038/s42254-023-00598-9","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","type":"journal_article","status":"public","publisher":"Springer Nature","date_updated":"2023-08-02T06:28:38Z","intvolume":"         5","month":"07","volume":5,"article_processing_charge":"No","citation":{"ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. 2023;5:379–397. doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>.","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” <i>Nature Reviews Physics</i>, vol. 5. Springer Nature, pp. 379–397, 2023.","mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 379–397, doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &#38; Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397."},"date_published":"2023-07-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2522-5820"]},"quality_controlled":"1","date_created":"2023-07-16T22:01:12Z"},{"date_published":"2023-07-05T00:00:00Z","file_date_updated":"2023-07-19T06:55:39Z","citation":{"chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>.","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. 2023;14(27):6309-6314. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>","ieee":"Y. Wei <i>et al.</i>, “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., &#38; Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314."},"month":"07","article_processing_charge":"Yes (via OA deal)","volume":14,"oa":1,"date_created":"2023-07-18T11:13:17Z","arxiv":1,"publication_identifier":{"eissn":["1948-7185"]},"quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"year":"2023","page":"6309-6314","_id":"13251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"intvolume":"        14","status":"public","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"type":"journal_article","publisher":"American Chemical Society","date_updated":"2025-04-23T13:01:50Z","doi":"10.1021/acs.jpclett.3c01158","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"content_type":"application/pdf","file_size":2121252,"success":1,"file_name":"2023_JourPhysChemistry_Wei.pdf","creator":"dernst","file_id":"13253","checksum":"c0c040063f06a51b9c463adc504f1a23","relation":"main_file","access_level":"open_access","date_updated":"2023-07-19T06:55:39Z","date_created":"2023-07-19T06:55:39Z"}],"external_id":{"arxiv":["2304.14198"],"pmid":["37405449"],"isi":["001022811500001"]},"author":[{"orcid":"0000-0001-8913-9719","last_name":"Wei","full_name":"Wei, Yujing","id":"0c5ff007-2600-11ee-b896-98bd8d663294","first_name":"Yujing"},{"orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","full_name":"Lorenc, Dusan","last_name":"Lorenc"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"first_name":"Osman M.","full_name":"Bakr, Osman M.","last_name":"Bakr"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"last_name":"Alpichshev","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203"}],"oa_version":"Published Version","ec_funded":1,"project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"day":"05","abstract":[{"lang":"eng","text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy."}],"ddc":["530"],"publication":"The Journal of Physical Chemistry Letters","issue":"27","scopus_import":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1"},{"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","file":[{"success":1,"file_name":"2023_npjclimate_Goswami.pdf","checksum":"e9967d436a83b8ffcc6f58782e1f7500","creator":"dernst","file_id":"13326","access_level":"open_access","relation":"main_file","date_updated":"2023-07-31T08:00:01Z","date_created":"2023-07-31T08:00:01Z","content_type":"application/pdf","file_size":1750712}],"department":[{"_id":"CaMu"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001024920300002"]},"author":[{"full_name":"Goswami, Bidyut B","last_name":"Goswami","first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b"},{"full_name":"An, Soon Il","first_name":"Soon Il","last_name":"An"}],"oa_version":"Published Version","publication":"npj Climate and Atmospheric Science","day":"08","abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"ddc":["550"],"publication_status":"published","scopus_import":"1","article_number":"82","has_accepted_license":"1","file_date_updated":"2023-07-31T08:00:01Z","date_published":"2023-07-08T00:00:00Z","article_processing_charge":"Yes","month":"07","volume":6,"oa":1,"citation":{"ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>.","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>npj Climate and Atmospheric Science</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>","apa":"GOSWAMI, B. B., &#38; An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>Npj Climate and Atmospheric Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>, vol. 6, 82, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>.","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” <i>npj Climate and Atmospheric Science</i>, vol. 6. Springer Nature, 2023."},"date_created":"2023-07-23T22:01:10Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["2397-3722"]},"_id":"13256","year":"2023","article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","status":"public","publisher":"Springer Nature","date_updated":"2023-08-02T06:38:07Z","intvolume":"         6","acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","doi":"10.1038/s41612-023-00411-5"},{"oa_version":"Preprint","abstract":[{"text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.","lang":"eng"}],"day":"15","publication":"Physical Review B","issue":"3","scopus_import":"1","publication_status":"published","article_number":"035111","title":"Magnetotropic susceptibility","department":[{"_id":"KiMo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.10038"}],"external_id":{"isi":["001062708600002"],"arxiv":["2208.10038"]},"author":[{"last_name":"Shekhter","first_name":"A.","full_name":"Shekhter, A."},{"first_name":"R. D.","full_name":"Mcdonald, R. D.","last_name":"Mcdonald"},{"full_name":"Ramshaw, B. J.","first_name":"B. J.","last_name":"Ramshaw"},{"orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","last_name":"Modic","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"}],"year":"2023","_id":"13257","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"intvolume":"       108","status":"public","type":"journal_article","publisher":"American Physical Society","date_updated":"2023-12-13T11:58:57Z","doi":"10.1103/PhysRevB.108.035111","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","date_published":"2023-07-15T00:00:00Z","citation":{"short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. <i>Physical Review B</i>. 2023;108(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>","chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>.","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” <i>Physical Review B</i>, vol. 108, no. 3. American Physical Society, 2023.","mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” <i>Physical Review B</i>, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>.","apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., &#38; Modic, K. A. (2023). Magnetotropic susceptibility. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>"},"month":"07","volume":108,"article_processing_charge":"No","oa":1,"date_created":"2023-07-23T22:01:10Z","arxiv":1,"quality_controlled":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"year":"2023","pmid":1,"_id":"13258","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","doi":"10.1038/s41467-023-39625-9","intvolume":"        14","publisher":"Springer Nature","status":"public","type":"journal_article","date_updated":"2025-04-14T07:43:55Z","citation":{"mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>.","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>.","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153."},"article_processing_charge":"Yes","volume":14,"month":"07","oa":1,"date_published":"2023-07-12T00:00:00Z","file_date_updated":"2023-07-31T11:32:36Z","quality_controlled":"1","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"date_created":"2023-07-23T22:01:11Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"ddc":["000"],"abstract":[{"text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.","lang":"eng"}],"day":"12","publication":"Nature Communications","oa_version":"Published Version","ec_funded":1,"has_accepted_license":"1","related_material":{"record":[{"id":"13336","status":"public","relation":"research_data"}]},"article_number":"4153","scopus_import":"1","corr_author":"1","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"KrCh"}],"file":[{"content_type":"application/pdf","file_size":1601682,"file_id":"13337","checksum":"5aceefdfe76686267b93ae4fe81899f1","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2023-07-31T11:32:36Z","date_created":"2023-07-31T11:32:36Z","success":1,"file_name":"2023_NatureComm_Kleshnina.pdf"}],"title":"The effect of environmental information on evolution of cooperation in stochastic games","author":[{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Simsa, Stepan","first_name":"Stepan","id":"409d615c-2f95-11ee-b934-90a352102c1e","last_name":"Simsa","orcid":"0000-0001-6687-1210"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"external_id":{"isi":["001029450400031"],"pmid":["37438341"]}},{"oa_version":"Published Version","abstract":[{"text":"Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.","lang":"eng"}],"day":"07","ddc":["580"],"issue":"27","publication":"Science Advances","scopus_import":"1","publication_status":"published","has_accepted_license":"1","title":"WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"date_created":"2023-08-01T06:40:35Z","relation":"main_file","date_updated":"2023-08-01T06:40:35Z","access_level":"open_access","creator":"dernst","checksum":"f59217e1083767777318b5d0cc5e141d","file_id":"13338","success":1,"file_name":"2023_ScienceAdvance_Ogura.pdf","file_size":1759993,"content_type":"application/pdf"}],"external_id":{"pmid":["37418524"],"isi":["001030983100012"]},"author":[{"first_name":"Nao","full_name":"Ogura, Nao","last_name":"Ogura"},{"full_name":"Sasagawa, Yohei","first_name":"Yohei","last_name":"Sasagawa"},{"last_name":"Ito","id":"d5a17a4a-e534-11eb-93ec-91fa2aa9bd57","first_name":"Tasuku","full_name":"Ito, Tasuku","orcid":"0000-0002-2482-9089"},{"first_name":"Toshiaki","full_name":"Tameshige, Toshiaki","last_name":"Tameshige"},{"last_name":"Kawai","first_name":"Satomi","full_name":"Kawai, Satomi"},{"full_name":"Sano, Masaki","first_name":"Masaki","last_name":"Sano"},{"full_name":"Doll, Yuki","first_name":"Yuki","last_name":"Doll"},{"first_name":"Akira","full_name":"Iwase, Akira","last_name":"Iwase"},{"full_name":"Kawamura, Ayako","first_name":"Ayako","last_name":"Kawamura"},{"first_name":"Takamasa","full_name":"Suzuki, Takamasa","last_name":"Suzuki"},{"full_name":"Nikaido, Itoshi","last_name":"Nikaido","first_name":"Itoshi"},{"full_name":"Sugimoto, Keiko","first_name":"Keiko","last_name":"Sugimoto"},{"first_name":"Momoko","last_name":"Ikeuchi","full_name":"Ikeuchi, Momoko"}],"pmid":1,"year":"2023","_id":"13259","page":"eadg6983","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","intvolume":"         9","date_updated":"2023-12-13T11:59:29Z","publisher":"American Association for the Advancement of Science","type":"journal_article","status":"public","doi":"10.1126/sciadv.adg6983","acknowledgement":"Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical support with tissue culture; and A. Furuta for technical support in bulk RNA-seq analysis. We also thank the Single-cell Omics Laboratory for technical consultation in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and 22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and by the Shiseido Female Researcher Science Grant to M.I. This work was partially supported by RIKENE pigenome Control Program, Medical Research Center Initiative for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.","date_published":"2023-07-07T00:00:00Z","file_date_updated":"2023-08-01T06:40:35Z","citation":{"ama":"Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. <i>Science Advances</i>. 2023;9(27):eadg6983. doi:<a href=\"https://doi.org/10.1126/sciadv.adg6983\">10.1126/sciadv.adg6983</a>","chicago":"Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.adg6983\">https://doi.org/10.1126/sciadv.adg6983</a>.","apa":"Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi, M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adg6983\">https://doi.org/10.1126/sciadv.adg6983</a>","ieee":"N. Ogura <i>et al.</i>, “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus,” <i>Science Advances</i>, vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983, 2023.","mla":"Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” <i>Science Advances</i>, vol. 9, no. 27, American Association for the Advancement of Science, 2023, p. eadg6983, doi:<a href=\"https://doi.org/10.1126/sciadv.adg6983\">10.1126/sciadv.adg6983</a>.","ista":"Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 9(27), eadg6983.","short":"N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll, A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science Advances 9 (2023) eadg6983."},"oa":1,"volume":9,"article_processing_charge":"Yes","month":"07","date_created":"2023-07-23T22:01:11Z","publication_identifier":{"eissn":["2375-2548"]},"quality_controlled":"1","language":[{"iso":"eng"}]},{"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"file":[{"content_type":"application/pdf","file_size":2382587,"checksum":"70de3c4878de6efe00dc56de2df8812f","file_id":"13339","creator":"dernst","date_created":"2023-08-01T06:58:34Z","date_updated":"2023-08-01T06:58:34Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2023_GBE_Barata.pdf"}],"external_id":{"isi":["001023444700003"],"pmid":["37341535"]},"author":[{"orcid":"0000-0003-1945-2245","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","last_name":"De Castro Barbosa Rodrigues Barata","first_name":"Carolina","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"full_name":"Snook, Rhonda R.","first_name":"Rhonda R.","last_name":"Snook"},{"last_name":"Ritchie","first_name":"Michael G.","full_name":"Ritchie, Michael G."},{"full_name":"Kosiol, Carolin","first_name":"Carolin","last_name":"Kosiol"}],"oa_version":"Published Version","ddc":["570"],"abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"day":"01","publication":"Genome biology and evolution","issue":"7","scopus_import":"1","corr_author":"1","publication_status":"published","related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"has_accepted_license":"1","article_number":"evad113","date_published":"2023-07-01T00:00:00Z","file_date_updated":"2023-08-01T06:58:34Z","citation":{"short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford University Press, 2023.","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>."},"article_processing_charge":"Yes","volume":15,"month":"07","oa":1,"date_created":"2023-07-23T22:01:11Z","publication_identifier":{"eissn":["1759-6653"]},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2023","pmid":1,"_id":"13260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"intvolume":"        15","type":"journal_article","publisher":"Oxford University Press","status":"public","date_updated":"2025-05-14T11:08:37Z","doi":"10.1093/gbe/evad113","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping."},{"department":[{"_id":"EdHa"}],"main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","author":[{"last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975"},{"full_name":"Chen, Hongtao","last_name":"Chen","first_name":"Hongtao"},{"first_name":"Lev","full_name":"Barinov, Lev","last_name":"Barinov"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"external_id":{"isi":["001106405600028"]},"day":"29","abstract":[{"text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.","lang":"eng"}],"project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"publication":"Science","issue":"6652","oa_version":"Preprint","scopus_import":"1","publication_status":"published","citation":{"chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>.","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362."},"oa":1,"month":"06","article_processing_charge":"No","volume":380,"date_published":"2023-06-29T00:00:00Z","quality_controlled":"1","publication_identifier":{"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"date_created":"2023-07-23T22:01:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","year":"2023","_id":"13261","page":"1357-1362","doi":"10.1126/science.adf5568","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","intvolume":"       380","date_updated":"2025-04-14T08:55:54Z","type":"journal_article","publisher":"American Association for the Advancement of Science","status":"public"}]