[{"day":"20","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-04-20T00:00:00Z","page":"211-228","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","citation":{"chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15"},"abstract":[{"text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"checksum":"60dcafc1b4f6f070be43bad3fe877974","success":1,"date_created":"2023-06-19T08:43:21Z","date_updated":"2023-06-19T08:43:21Z","relation":"main_file","file_id":"13151","file_size":521425,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_Anand.pdf"}],"status":"public","ddc":["000"],"title":"Computing adequately permissive assumptions for synthesis","intvolume":" 13994","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13141","month":"04","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-031-30820-8_15","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-06-19T08:43:21Z","date_updated":"2023-06-19T08:49:46Z","date_created":"2023-06-18T22:00:47Z","volume":13994,"author":[{"first_name":"Ashwani","last_name":"Anand","full_name":"Anand, Ashwani"},{"full_name":"Mallik, Kaushik","first_name":"Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475"},{"full_name":"Nayak, Satya Prakash","last_name":"Nayak","first_name":"Satya Prakash"},{"full_name":"Schmuck, Anne Kathrin","last_name":"Schmuck","first_name":"Anne Kathrin"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"year":"2023"},{"citation":{"ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023."},"page":"106","date_published":"2023-04-18T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"18","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12826","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","ddc":["570","571"],"status":"public","file":[{"checksum":"5f589a9af025f7eeebfd0c186209913e","date_created":"2023-04-20T09:14:38Z","date_updated":"2023-04-20T09:26:51Z","file_id":"12857","relation":"source_file","creator":"vpokusae","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14507243,"access_level":"closed","file_name":"Thesis_Pokusaeva.docx"},{"checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"date_created":"2023-04-20T09:14:44Z","date_updated":"2023-04-20T09:14:44Z","relation":"main_file","file_id":"12858","content_type":"application/pdf","file_size":10090711,"creator":"vpokusae","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.15479/at:ista:12826","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"month":"04","year":"2023","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria"}],"date_updated":"2023-06-23T09:47:36Z","date_created":"2023-04-14T14:56:04Z","ec_funded":1,"file_date_updated":"2023-04-20T09:26:51Z"},{"article_type":"original","page":"277-295","publication":"Algorithmica","citation":{"mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6"},"date_published":"2023-01-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","status":"public","ddc":["510"],"intvolume":" 85","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"12086","oa_version":"Published Version","file":[{"success":1,"checksum":"71685ca5121f4c837f40c3f8eb50c915","date_updated":"2023-01-20T10:02:48Z","date_created":"2023-01-20T10:02:48Z","file_id":"12322","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":911017,"access_level":"open_access","file_name":"2023_Algorithmica_Edelsbrunner.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"isi":1,"quality_controlled":"1","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000846967100001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00453-022-01027-6","month":"01","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","year":"2023","date_created":"2022-09-11T22:01:57Z","date_updated":"2023-06-27T12:53:43Z","volume":85,"author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F"}],"file_date_updated":"2023-01-20T10:02:48Z","ec_funded":1},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"year":"2023","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","date_updated":"2023-06-28T11:54:35Z","date_created":"2023-01-08T23:00:53Z","volume":23,"author":[{"first_name":"Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo"},{"full_name":"Wirth, Melchior","first_name":"Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241"}],"article_number":"9","file_date_updated":"2023-01-20T10:45:06Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208"},{"grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups"}],"external_id":{"isi":["000906214600004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00028-022-00859-7","month":"01","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"ddc":["510"],"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","status":"public","intvolume":" 23","_id":"12104","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"dernst","file_size":422612,"content_type":"application/pdf","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access","date_created":"2023-01-20T10:45:06Z","date_updated":"2023-01-20T10:45:06Z","success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","file_id":"12325","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces."}],"issue":"1","article_type":"original","publication":"Journal of Evolution Equations","citation":{"ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7."},"date_published":"2023-01-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"author":[{"first_name":"Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"Goswami, Bidyut B"}],"related_material":{"link":[{"url":" https://doi.org/10.1007/s00382-022-06401-2","relation":"erratum"}]},"date_updated":"2023-06-28T11:49:58Z","date_created":"2022-06-05T22:01:50Z","volume":60,"acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). 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 Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaMu"}],"doi":"10.1007/s00382-022-06337-7","language":[{"iso":"eng"}],"external_id":{"isi":["000803119400002"]},"isi":1,"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"oa_version":"None","_id":"11434","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","intvolume":" 60","abstract":[{"text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.","lang":"eng"}],"type":"journal_article","date_published":"2023-01-01T00:00:00Z","publication":"Climate Dynamics","citation":{"ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7."},"article_type":"original","page":"427-442","day":"01","article_processing_charge":"No","scopus_import":"1"},{"_id":"12467","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Quantitative safety and liveness","status":"public","ddc":["000"],"intvolume":" 13992","file":[{"relation":"main_file","file_id":"12468","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"date_created":"2023-01-31T07:22:21Z","date_updated":"2023-01-31T07:22:21Z","access_level":"open_access","file_name":"qsl.pdf","file_size":449027,"content_type":"application/pdf","creator":"esarac"},{"checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","success":1,"date_updated":"2023-06-19T10:28:09Z","date_created":"2023-06-19T10:28:09Z","relation":"main_file","file_id":"13153","file_size":1048171,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_HenzingerT.pdf"}],"oa_version":"Published Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"publication":"26th International Conference Foundations of Software Science and Computation Structures","citation":{"short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370."},"page":"349-370","date_published":"2023-04-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","year":"2023","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Springer Nature","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"date_created":"2023-01-31T07:23:56Z","date_updated":"2023-07-14T11:20:27Z","volume":13992,"file_date_updated":"2023-06-19T10:28:09Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2301.11175"]},"quality_controlled":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"conference":{"end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22","name":"FOSSACS: Foundations of Software Science and Computation Structures"},"doi":"10.1007/978-3-031-30829-1_17","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308284"],"issn":["0302-9743"]}},{"doi":"10.1145/3591230","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publication_identifier":{"eissn":["2475-1421"]},"month":"06","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval"},{"full_name":"Khalanskiy, Dmitry","last_name":"Khalanskiy","first_name":"Dmitry"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"volume":7,"date_updated":"2023-07-17T08:43:19Z","date_created":"2023-07-02T22:00:43Z","year":"2023","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery ","publication_status":"published","file_date_updated":"2023-07-03T13:09:39Z","article_number":"116","date_published":"2023-06-06T00:00:00Z","citation":{"ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230."},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_ACMProgram.Lang._Koval.pdf","creator":"alisjak","content_type":"application/pdf","file_size":1266773,"file_id":"13187","relation":"main_file","success":1,"checksum":"5dba6e73f0ed79adbdae14d165bc2f68","date_updated":"2023-07-03T13:09:39Z","date_created":"2023-07-03T13:09:39Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13179","intvolume":" 7","status":"public","ddc":["000"],"title":"CQS: A formally-verified framework for fair and abortable synchronization","abstract":[{"lang":"eng","text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives."}],"type":"journal_article"},{"publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"TiBr"}],"year":"2023","date_updated":"2023-07-17T08:39:19Z","date_created":"2023-07-02T22:00:43Z","volume":16,"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"first_name":"Julian","last_name":"Lyczak","id":"3572849A-F248-11E8-B48F-1D18A9856A87","full_name":"Lyczak, Julian"},{"last_name":"Sarapin","first_name":"Roman","full_name":"Sarapin, Roman"}],"quality_controlled":"1","external_id":{"arxiv":["2203.06881"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.06881"}],"language":[{"iso":"eng"}],"doi":"10.2140/involve.2023.16.331","month":"05","publication_identifier":{"issn":["1944-4176"],"eissn":["1944-4184"]},"status":"public","title":"Local solubility for a family of quadrics over a split quadric surface","intvolume":" 16","_id":"13180","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface"}],"issue":"2","article_type":"original","page":"331-342","publication":"Involve","citation":{"ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331."},"date_published":"2023-05-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"No"},{"day":"01","month":"07","has_accepted_license":"1","article_processing_charge":"No","conference":{"start_date":"2023-06-12","location":"Maribor, Slovenia","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"date_published":"2023-07-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.","mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42."},"quality_controlled":"1","page":"42-42","file_date_updated":"2023-07-18T09:28:30Z","type":"conference_abstract","author":[{"full_name":"Elefante, Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano"},{"full_name":"Stadlbauer, Stephan","first_name":"Stephan","last_name":"Stadlbauer","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alexander, Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael F","last_name":"Alexander"},{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"}],"date_created":"2023-06-23T11:03:18Z","date_updated":"2023-07-18T09:32:16Z","file":[{"checksum":"0ab6173cd5c5634ed773cd37ff012681","success":1,"date_created":"2023-07-18T09:28:30Z","date_updated":"2023-07-18T09:28:30Z","relation":"main_file","file_id":"13250","file_size":380354,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_ASHPC_Elefante.pdf"}],"oa_version":"Submitted Version","year":"2023","_id":"13162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Cryo-EM software packages: A sys-admins point of view","status":"public","publication_status":"accepted","ddc":["000"],"publisher":"EuroCC","department":[{"_id":"ScienComp"}]},{"ddc":["000"],"title":"Running Windows-applications on a Linux HPC cluster using WINE","status":"public","_id":"13161","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","content_type":"application/pdf","file_size":316959,"file_name":"2023_ASHPC_Schloegl.pdf","access_level":"open_access","date_created":"2023-07-18T09:18:55Z","date_updated":"2023-07-18T09:18:55Z","success":1,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_id":"13249","relation":"main_file"}],"oa_version":"Submitted Version","type":"conference_abstract","page":"59-59","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","citation":{"ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d."},"date_published":"2023-07-01T00:00:00Z","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication_status":"inpress","publisher":"EuroCC","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"year":"2023","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","date_updated":"2023-07-18T09:30:54Z","date_created":"2023-06-23T11:01:23Z","author":[{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano","full_name":"Elefante, Stefano"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-07-18T09:18:55Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","start_date":"2023-06-13","end_date":"2023-06-15"},"month":"07"},{"day":"05","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"date_published":"2023-07-05T00:00:00Z","publication":"The Journal of Physical Chemistry Letters","citation":{"mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","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.","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.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158","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.","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., 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. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158"},"article_type":"original","page":"6309-6314","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."}],"issue":"27","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_JourPhysChemistry_Wei.pdf","access_level":"open_access","file_size":2121252,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13253","date_created":"2023-07-19T06:55:39Z","date_updated":"2023-07-19T06:55:39Z","checksum":"c0c040063f06a51b9c463adc504f1a23","success":1}],"_id":"13251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","ddc":["530"],"status":"public","intvolume":" 14","month":"07","publication_identifier":{"eissn":["1948-7185"]},"doi":"10.1021/acs.jpclett.3c01158","language":[{"iso":"eng"}],"external_id":{"isi":["001022811500001"],"arxiv":["2304.14198"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"file_date_updated":"2023-07-19T06:55:39Z","ec_funded":1,"author":[{"full_name":"Wei, Yujing","orcid":"0000-0001-8913-9719","id":"0c5ff007-2600-11ee-b896-98bd8d663294","last_name":"Wei","first_name":"Yujing"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc","full_name":"Lorenc, Dusan"},{"last_name":"Zhumekenov","first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-07-18T11:13:17Z","date_updated":"2023-07-19T06:59:19Z","volume":14,"year":"2023","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.","publication_status":"published","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"publisher":"American Chemical Society"},{"date_created":"2023-07-24T15:11:41Z","date_updated":"2023-07-31T08:38:38Z","volume":261,"author":[{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Kebis","first_name":"Pavol","full_name":"Kebis, Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","file_date_updated":"2023-07-24T15:11:05Z","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.129","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.03447"]},"month":"07","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"file":[{"file_id":"13293","relation":"main_file","success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2","date_updated":"2023-07-24T15:11:05Z","date_created":"2023-07-24T15:11:05Z","access_level":"open_access","file_name":"icalp23.pdf","creator":"esarac","file_size":859379,"content_type":"application/pdf"}],"oa_version":"Published Version","status":"public","ddc":["000"],"title":"Regular methods for operator precedence languages","intvolume":" 261","_id":"13292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2023-07-05T00:00:00Z","page":"129:1--129:20","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20."},"day":"05","article_processing_charge":"Yes","has_accepted_license":"1"},{"date_published":"2023-04-14T00:00:00Z","article_type":"original","publication":"SciPost Physics Core","citation":{"ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029."},"day":"14","has_accepted_license":"1","article_processing_charge":"No","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"file":[{"file_name":"2023_SciPostPhysCore_Tucci.pdf","access_level":"open_access","file_size":523236,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13329","date_updated":"2023-07-31T09:02:27Z","date_created":"2023-07-31T09:02:27Z","checksum":"b472bc82108747eda5d52adf9e2ac7f3","success":1}],"oa_version":"Published Version","status":"public","ddc":["530"],"title":"Stochastic representation of the quantum quartic oscillator","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13277","abstract":[{"lang":"eng","text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results."}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.21468/scipostphyscore.6.2.029","quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2211.01923"]},"month":"04","publication_identifier":{"issn":["2666-9366"]},"date_created":"2023-07-24T10:47:46Z","date_updated":"2023-07-31T09:03:28Z","volume":6,"author":[{"full_name":"Tucci, Gennaro","last_name":"Tucci","first_name":"Gennaro"},{"full_name":"De Nicola, Stefano","last_name":"De Nicola","first_name":"Stefano","orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wald, Sascha","first_name":"Sascha","last_name":"Wald"},{"last_name":"Gambassi","first_name":"Andrea","full_name":"Gambassi, Andrea"}],"publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","year":"2023","file_date_updated":"2023-07-31T09:02:27Z","ec_funded":1,"article_number":"029"},{"has_accepted_license":"1","article_processing_charge":"No","day":"19","article_type":"original","citation":{"chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12"},"publication":"SciPost Physics Codebases","date_published":"2023-04-19T00:00:00Z","type":"journal_article","abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","ddc":["530"],"status":"public","_id":"13276","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13330","date_created":"2023-07-31T09:09:23Z","date_updated":"2023-07-31T09:09:23Z","checksum":"f583a70fe915d2208c803f5afb426daa","success":1,"file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","access_level":"open_access","content_type":"application/pdf","file_size":551418,"creator":"dernst"}],"publication_identifier":{"issn":["2949-804X"]},"month":"04","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2202.04603"]},"language":[{"iso":"eng"}],"doi":"10.21468/scipostphyscodeb.12","article_number":"12","ec_funded":1,"file_date_updated":"2023-07-31T09:09:23Z","department":[{"_id":"MiLe"}],"publisher":"SciPost Foundation","publication_status":"published","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","year":"2023","date_created":"2023-07-24T10:47:15Z","date_updated":"2023-07-31T09:16:02Z","related_material":{"record":[{"id":"13275","status":"public","relation":"research_data"}]},"author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"last_name":"Huber","first_name":"David","full_name":"Huber, David"},{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}]},{"date_published":"2023-04-19T00:00:00Z","doi":"10.21468/scipostphyscodeb.12-r1.0","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"oa":1,"citation":{"short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0.","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0."},"main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"article_processing_charge":"No","month":"04","day":"19","oa_version":"Published Version","date_updated":"2023-07-31T09:16:02Z","date_created":"2023-07-24T10:46:23Z","related_material":{"record":[{"id":"13276","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Lukas","last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MiLe"}],"publisher":"SciPost Foundation","ddc":["530"],"status":"public","title":"Codebase release 1.0 for FermiFCI","_id":"13275","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","ec_funded":1,"abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"type":"research_data_reference"},{"publication_identifier":{"isbn":["9781450395458"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1145/3558481.3591082","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2023-06-19","start_date":"2023-06-17","location":"Orlando, FL, United States"},"quality_controlled":"1","external_id":{"arxiv":["2304.09331"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-23T22:01:12Z","date_updated":"2023-07-31T10:54:32Z","author":[{"first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander"},{"full_name":"Hashemi, Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","last_name":"Hashemi","first_name":"Diba"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","publication_status":"published","year":"2023","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2023-06-17T00:00:00Z","page":"261-271","citation":{"apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082."},"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"type":"conference","file":[{"content_type":"application/pdf","file_size":2087937,"creator":"dernst","file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access","date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-31T10:53:08Z","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"relation":"main_file","file_id":"13334"}],"oa_version":"Published Version","ddc":["000"],"status":"public","title":"Provably-efficient and internally-deterministic parallel Union-Find","_id":"13262","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"issue":"2","ddc":["576"],"title":"Ten years of demographic modelling of divergence and speciation in the sea","status":"public","intvolume":" 16","_id":"11479","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"d4d6fa9ddf36643af994a6a757919afb","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","file_id":"12685","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2269822,"access_level":"open_access","file_name":"2023_EvolutionaryApplications_DeJode.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"542-559","publication":"Evolutionary Applications","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428."},"date_published":"2023-02-01T00:00:00Z","file_date_updated":"2023-02-27T07:10:17Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","year":"2023","date_updated":"2023-08-01T12:25:44Z","date_created":"2022-07-03T22:01:33Z","volume":16,"author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"month":"02","publication_identifier":{"eissn":["1752-4571"]},"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000815663700001"]},"language":[{"iso":"eng"}],"doi":"10.1111/eva.13428"},{"doi":"10.1038/s41598-022-19827-9","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001003345000051"]},"isi":1,"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["2045-2322"]},"author":[{"full_name":"Gómez, Arturo","first_name":"Arturo","last_name":"Gómez"},{"full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","first_name":"Goncalo","last_name":"Oliveira"}],"date_updated":"2023-08-01T12:31:40Z","date_created":"2023-01-22T23:00:55Z","volume":13,"year":"2023","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","file_date_updated":"2023-01-23T07:53:23Z","article_number":"468","date_published":"2023-01-10T00:00:00Z","publication":"Scientific Reports","citation":{"ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9."},"article_type":"original","day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"success":1,"checksum":"a8b83739f4a951e83e0b2a778f03b327","date_updated":"2023-01-23T07:53:23Z","date_created":"2023-01-23T07:53:23Z","file_id":"12336","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2167792,"access_level":"open_access","file_name":"2023_ScientificReports_Gomez.pdf"}],"oa_version":"Published Version","_id":"12329","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["510"],"title":"New approaches to epidemic modeling on networks","status":"public","intvolume":" 13","abstract":[{"text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection.","lang":"eng"}],"type":"journal_article"},{"date_updated":"2023-08-01T12:23:55Z","date_created":"2021-01-22T09:31:09Z","volume":2023,"author":[{"orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch","first_name":"Florian Alexander","full_name":"Wilsch, Florian Alexander"}],"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"TiBr"}],"year":"2023","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","month":"04","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnac048","quality_controlled":"1","isi":1,"external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"issue":"8","type":"journal_article","oa_version":"Preprint","title":"Integral points of bounded height on a log Fano threefold","status":"public","intvolume":" 2023","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9034","day":"01","article_processing_charge":"No","date_published":"2023-04-01T00:00:00Z","article_type":"original","page":"6780-6808","publication":"International Mathematics Research Notices","citation":{"apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048."}},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","creator":"dernst","file_size":4866332,"content_type":"application/pdf","file_id":"12843","relation":"main_file","success":1,"checksum":"cd52292963acce1111634d9fac08c699","date_updated":"2023-04-17T07:49:09Z","date_created":"2023-04-17T07:49:09Z"}],"intvolume":" 14","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","status":"public","ddc":["570"],"_id":"12469","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-16T00:00:00Z","article_type":"original","citation":{"chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002"},"publication":"Frontiers in Microbiology","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"16","scopus_import":"1","volume":14,"date_created":"2023-01-31T08:13:40Z","date_updated":"2023-08-01T12:39:58Z","author":[{"full_name":"Viljakainen, Lumi","last_name":"Viljakainen","first_name":"Lumi"},{"last_name":"Fürst","first_name":"Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"last_name":"Jurvansuu","first_name":"Jaana","full_name":"Jurvansuu, Jaana"},{"orcid":"0000-0001-7425-2372","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","last_name":"Oh","first_name":"Jinook","full_name":"Oh, Jinook"},{"full_name":"Tolonen, Lassi","last_name":"Tolonen","first_name":"Lassi"},{"full_name":"Eder, Thomas","first_name":"Thomas","last_name":"Eder"},{"last_name":"Rattei","first_name":"Thomas","full_name":"Rattei, Thomas"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"publisher":"Frontiers","department":[{"_id":"SyCr"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","file_date_updated":"2023-04-17T07:49:09Z","article_number":"1119002","language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1119002","project":[{"grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425","name":"Viral pathogens and social immunity in ants","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000961542100001"],"pmid":["PPR559293 "]},"publication_identifier":{"eissn":["1664-302X"]},"month":"03"},{"file":[{"file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","access_level":"open_access","content_type":"application/pdf","file_size":582850,"creator":"dernst","relation":"main_file","file_id":"12488","date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z","checksum":"46352e0ee71e460848f88685ca852681","success":1}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12287","ddc":["510"],"status":"public","title":"Local criteria for triangulating general manifolds","intvolume":" 69","abstract":[{"text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use.","lang":"eng"}],"type":"journal_article","date_published":"2023-01-01T00:00:00Z","publication":"Discrete & Computational Geometry","citation":{"chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7"},"article_type":"original","page":"156-191","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"author":[{"full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"full_name":"Wintraecken, Mathijs","first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"date_updated":"2023-08-01T12:47:32Z","date_created":"2023-01-16T10:04:06Z","volume":69,"year":"2023","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","file_date_updated":"2023-02-02T11:01:10Z","ec_funded":1,"doi":"10.1007/s00454-022-00431-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000862193600001"]},"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"month":"01","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]}},{"type":"journal_article","abstract":[{"text":"It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.","lang":"eng"}],"status":"public","title":"Directed percolation and the transition to turbulence","intvolume":" 5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12165","oa_version":"None","keyword":["General Physics and Astronomy"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"62-72","publication":"Nature Reviews Physics","citation":{"short":"B. Hof, Nature Reviews Physics 5 (2023) 62–72.","mla":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 62–72, doi:10.1038/s42254-022-00539-y.","chicago":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-022-00539-y.","ama":"Hof B. Directed percolation and the transition to turbulence. Nature Reviews Physics. 2023;5:62-72. doi:10.1038/s42254-022-00539-y","ieee":"B. Hof, “Directed percolation and the transition to turbulence,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 62–72, 2023.","apa":"Hof, B. (2023). Directed percolation and the transition to turbulence. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-022-00539-y","ista":"Hof B. 2023. Directed percolation and the transition to turbulence. Nature Reviews Physics. 5, 62–72."},"date_published":"2023-01-01T00:00:00Z","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","year":"2023","date_updated":"2023-08-01T12:50:48Z","date_created":"2023-01-12T12:10:18Z","volume":5,"author":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"month":"01","publication_identifier":{"eissn":["2522-5820"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000890148700002"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42254-022-00539-y"},{"intvolume":" 51","ddc":["570"],"title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","status":"public","_id":"12421","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","file_size":10045006,"access_level":"open_access","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","success":1,"checksum":"4e7069845e3dad22bb44fb71ec624c60","date_created":"2023-03-16T07:58:16Z","date_updated":"2023-03-16T07:58:16Z","file_id":"12728","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.","lang":"eng"}],"page":"87-99","article_type":"original","citation":{"chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221"},"publication":"Biochemical Society Transactions","date_published":"2023-02-01T00:00:00Z","keyword":["Biochemistry"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","department":[{"_id":"FlSc"}],"publisher":"Portland Press","publication_status":"published","year":"2023","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","volume":51,"date_updated":"2023-08-01T12:55:32Z","date_created":"2023-01-27T10:08:19Z","author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian"},{"full_name":"Javoor, Manjunath","last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"file_date_updated":"2023-03-16T07:58:16Z","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000926043100001"]},"language":[{"iso":"eng"}],"doi":"10.1042/bst20220221","publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"month":"02"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"10","article_type":"original","citation":{"short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10."},"publication":"Journal of Fluid Mechanics","date_published":"2023-01-10T00:00:00Z","type":"journal_article","abstract":[{"text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion.","lang":"eng"}],"intvolume":" 954","ddc":["530"],"status":"public","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12105","file":[{"date_created":"2023-02-02T12:34:54Z","date_updated":"2023-02-02T12:34:54Z","success":1,"checksum":"9224f987caefe5dd85a70814d3cce65c","file_id":"12489","relation":"main_file","creator":"dernst","file_size":1931647,"content_type":"application/pdf","file_name":"2023_JourFluidMechanics_Marensi.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"month":"01","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000903336600001"],"arxiv":["2101.07516"]},"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2022.1001","article_number":"A10","file_date_updated":"2023-02-02T12:34:54Z","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","year":"2023","volume":954,"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-01T12:53:23Z","author":[{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","last_name":"Marensi","full_name":"Marensi, Elena"},{"orcid":"0000-0002-8490-9312","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","last_name":"Yalniz","first_name":"Gökhan","full_name":"Yalniz, Gökhan"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"}]},{"page":"318-328","article_type":"original","citation":{"ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328."},"publication":"Evolution: International journal of organic evolution","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 77","title":"A multivariate view of the speciation continuum","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12514","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/evolut/qpac004","publication_identifier":{"eissn":["1558-5646"]},"month":"01","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","volume":77,"date_created":"2023-02-05T23:00:59Z","date_updated":"2023-08-01T12:58:30Z","author":[{"last_name":"Bolnick","first_name":"Daniel I.","full_name":"Bolnick, Daniel I."},{"first_name":"Amanda K.","last_name":"Hund","full_name":"Hund, Amanda K."},{"first_name":"Patrik","last_name":"Nosil","full_name":"Nosil, Patrik"},{"first_name":"Foen","last_name":"Peng","full_name":"Peng, Foen"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Subramanian, Swapna","last_name":"Subramanian","first_name":"Swapna"},{"full_name":"Wolf, Jochen B.W.","last_name":"Wolf","first_name":"Jochen B.W."},{"last_name":"Yukilevich","first_name":"Roman","full_name":"Yukilevich, Roman"}]},{"file_date_updated":"2023-02-14T07:58:26Z","article_number":"00093","author":[{"full_name":"Forghani, Mohammad","last_name":"Forghani","first_name":"Mohammad"},{"full_name":"Claramunt, Christophe","last_name":"Claramunt","first_name":"Christophe"},{"full_name":"Karimipour, Farid","last_name":"Karimipour","first_name":"Farid","orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425"},{"full_name":"Heiler, Georg","last_name":"Heiler","first_name":"Georg"}],"date_created":"2023-02-14T07:56:21Z","date_updated":"2023-08-01T13:15:48Z","year":"2023","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Institute of Electrical and Electronics Engineers","month":"02","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"conference":{"location":"Orlando, FL, United States","start_date":"2022-11-28","end_date":"2022-12-01","name":"ICDMW: Conference on Data Mining Workshops"},"doi":"10.1109/icdmw58026.2022.00093","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000971492200145"]},"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"type":"conference","oa_version":"Submitted Version","file":[{"file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","access_level":"open_access","file_size":1183339,"content_type":"application/pdf","creator":"fkarimip","relation":"main_file","file_id":"12549","date_updated":"2023-02-14T07:58:26Z","date_created":"2023-02-14T07:58:26Z","checksum":"c253bee25e6dfe484f96662daa119cb6","success":1}],"_id":"12548","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","ddc":["600"],"day":"08","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-02-08T00:00:00Z","publication":"2022 IEEE International Conference on Data Mining Workshops","citation":{"mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023."}},{"ec_funded":1,"year":"2023","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Society for Industrial & Applied Mathematics","author":[{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"full_name":"Opršal, Jakub","first_name":"Jakub","last_name":"Opršal","id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456"},{"full_name":"Wrochna, Marcin","last_name":"Wrochna","first_name":"Marcin"},{"first_name":"Stanislav","last_name":"Živný","full_name":"Živný, Stanislav"}],"date_created":"2023-02-16T07:03:52Z","date_updated":"2023-08-01T13:11:30Z","volume":52,"month":"01","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"oa":1,"external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2003.11351","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"doi":"10.1137/20m1378223","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"issue":"1","_id":"12563","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Topology and adjunction in promise constraint satisfaction","status":"public","intvolume":" 52","oa_version":"Preprint","scopus_import":"1","keyword":["General Mathematics","General Computer Science"],"day":"01","article_processing_charge":"No","publication":"SIAM Journal on Computing","citation":{"ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223."},"article_type":"original","page":"38-79","date_published":"2023-01-01T00:00:00Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevE.107.014608","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"month":"01","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","year":"2023","department":[{"_id":"GradSch"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Rojas Vega, Mauricio Nicolas","last_name":"Rojas Vega","first_name":"Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d"},{"full_name":"De Castro, Pablo","first_name":"Pablo","last_name":"De Castro"},{"full_name":"Soto, Rodrigo","first_name":"Rodrigo","last_name":"Soto"}],"volume":107,"date_updated":"2023-08-01T13:09:45Z","date_created":"2023-02-12T23:00:59Z","article_number":"014608","citation":{"chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608"},"publication":"Physical Review E","article_type":"original","date_published":"2023-01-24T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"24","_id":"12545","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 107","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","status":"public","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.","lang":"eng"}]},{"month":"01","publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03013498/"}],"external_id":{"isi":["000898440000001"]},"quality_controlled":"1","isi":1,"doi":"10.1090/proc/15239","language":[{"iso":"eng"}],"year":"2023","publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"American Mathematical Society","author":[{"full_name":"Balestrieri, Francesca","first_name":"Francesca","last_name":"Balestrieri","id":"3ACCD756-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-01-29T23:00:58Z","date_updated":"2023-08-01T13:03:32Z","volume":151,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Proceedings of the American Mathematical Society","citation":{"short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239.","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239.","ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914."},"article_type":"original","page":"907-914","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent."}],"issue":"3","_id":"12427","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","status":"public","intvolume":" 151","oa_version":"Preprint"},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"letter_note","page":"291-293","publication":"Neuron","citation":{"ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","apa":"Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006","chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006.","mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293."},"date_published":"2023-02-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}],"issue":"3","title":"Going back in time with TEMPO","status":"public","intvolume":" 111","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12542","oa_version":"None","month":"02","publication_identifier":{"eissn":["1097-4199"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000994473300001"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2023.01.006","publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"year":"2023","date_created":"2023-02-12T23:00:58Z","date_updated":"2023-08-01T13:10:27Z","volume":111,"author":[{"first_name":"Ana","last_name":"Villalba Requena","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12567","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","status":"public","ddc":["570"],"intvolume":" 24","file":[{"date_created":"2023-02-20T07:09:27Z","date_updated":"2023-02-20T07:09:27Z","checksum":"69a35dcd3e0249f902ab881b06ee2e58","success":1,"relation":"main_file","file_id":"12569","content_type":"application/pdf","file_size":2823025,"creator":"dernst","file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.","lang":"eng"}],"issue":"3","publication":"International Journal of Molecular Sciences","citation":{"apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128."},"article_type":"original","date_published":"2023-01-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","year":"2023","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"MDPI","author":[{"full_name":"Mrestani, Achmed","first_name":"Achmed","last_name":"Mrestani"},{"id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina","last_name":"Lichter","full_name":"Lichter, Katharina"},{"last_name":"Sirén","first_name":"Anna Leena","full_name":"Sirén, Anna Leena"},{"last_name":"Heckmann","first_name":"Manfred","full_name":"Heckmann, Manfred"},{"full_name":"Paul, Mila M.","first_name":"Mila M.","last_name":"Paul"},{"last_name":"Pauli","first_name":"Martin","full_name":"Pauli, Martin"}],"date_updated":"2023-08-01T13:16:36Z","date_created":"2023-02-19T23:00:56Z","volume":24,"article_number":"2128","file_date_updated":"2023-02-20T07:09:27Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000930324700001"]},"isi":1,"quality_controlled":"1","doi":"10.3390/ijms24032128","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1422-0067"]}},{"ec_funded":1,"file_date_updated":"2023-02-20T07:30:20Z","article_number":"113733","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel"}],"volume":948,"date_created":"2023-02-19T23:00:55Z","date_updated":"2023-08-01T13:17:20Z","year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","publisher":"Elsevier","department":[{"_id":"DaAl"}],"publication_status":"published","publication_identifier":{"issn":["0304-3975"]},"month":"02","doi":"10.1016/j.tcs.2023.113733","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000934262700001"]},"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","grant_number":"840605","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","issue":"2","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"b27c5290f2f1500c403494364ee39c9f","success":1,"date_created":"2023-02-20T07:30:20Z","date_updated":"2023-02-20T07:30:20Z","relation":"main_file","file_id":"12570","file_size":602333,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_TheoreticalCompScience_Alistarh.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12566","intvolume":" 948","ddc":["000"],"title":"Wait-free approximate agreement on graphs","status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"28","scopus_import":"1","date_published":"2023-02-28T00:00:00Z","citation":{"ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023)."},"publication":"Theoretical Computer Science","article_type":"original"},{"_id":"12681","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"status":"public","title":"Elasto-inertial turbulence","intvolume":" 55","oa_version":"Published Version","file":[{"file_id":"12690","relation":"main_file","success":1,"checksum":"2666aa3af2a25252d35eb8681d3edff7","date_created":"2023-02-27T09:23:02Z","date_updated":"2023-02-27T09:23:02Z","access_level":"open_access","file_name":"2023_AnnReviewFluidMech_Dubief.pdf","creator":"dernst","file_size":4036706,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT.","lang":"eng"}],"issue":"1","publication":"Annual Review of Fluid Mechanics","citation":{"short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705."},"article_type":"original","page":"675-705","date_published":"2023-01-19T00:00:00Z","scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","year":"2023","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Annual Reviews","author":[{"last_name":"Dubief","first_name":"Yves","full_name":"Dubief, Yves"},{"first_name":"Vincent E.","last_name":"Terrapon","full_name":"Terrapon, Vincent E."},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-01T13:19:47Z","date_created":"2023-02-26T23:01:01Z","volume":55,"file_date_updated":"2023-02-27T09:23:02Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000915418100026"]},"isi":1,"quality_controlled":"1","doi":"10.1146/annurev-fluid-032822-025933","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]}},{"has_accepted_license":"1","article_processing_charge":"No","day":"19","scopus_import":"1","date_published":"2023-01-19T00:00:00Z","citation":{"ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023.","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957","ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602."},"publication":"Annual Review of Fluid Mechanics","page":"575-602","article_type":"original","abstract":[{"lang":"eng","text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":4769537,"content_type":"application/pdf","file_name":"2023_AnnReviewFluidMech_Avila.pdf","access_level":"open_access","date_updated":"2023-02-27T09:35:52Z","date_created":"2023-02-27T09:35:52Z","success":1,"checksum":"f99ef30f76cabc9e5e1946b380c16db4","file_id":"12691","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12682","intvolume":" 55","ddc":["530"],"status":"public","title":"Transition to turbulence in pipe flow","publication_identifier":{"issn":["0066-4189"]},"month":"01","doi":"10.1146/annurev-fluid-120720-025957","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000915418100023"]},"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"quality_controlled":"1","isi":1,"file_date_updated":"2023-02-27T09:35:52Z","author":[{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"last_name":"Barkley","first_name":"Dwight","full_name":"Barkley, Dwight"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"volume":55,"date_updated":"2023-08-01T13:20:30Z","date_created":"2023-02-26T23:01:01Z","year":"2023","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","department":[{"_id":"BjHo"}],"publisher":"Annual Reviews","publication_status":"published"},{"ec_funded":1,"file_date_updated":"2023-03-07T09:19:41Z","author":[{"full_name":"Araújo, Nuno A.M.","first_name":"Nuno A.M.","last_name":"Araújo"},{"full_name":"Janssen, Liesbeth M.C.","last_name":"Janssen","first_name":"Liesbeth M.C."},{"full_name":"Barois, Thomas","first_name":"Thomas","last_name":"Barois"},{"full_name":"Boffetta, Guido","first_name":"Guido","last_name":"Boffetta"},{"first_name":"Itai","last_name":"Cohen","full_name":"Cohen, Itai"},{"first_name":"Alessandro","last_name":"Corbetta","full_name":"Corbetta, Alessandro"},{"last_name":"Dauchot","first_name":"Olivier","full_name":"Dauchot, Olivier"},{"first_name":"Marjolein","last_name":"Dijkstra","full_name":"Dijkstra, Marjolein"},{"last_name":"Durham","first_name":"William M.","full_name":"Durham, William M."},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"},{"full_name":"Garnier, Simon","last_name":"Garnier","first_name":"Simon"},{"full_name":"Gelderblom, Hanneke","last_name":"Gelderblom","first_name":"Hanneke"},{"full_name":"Golestanian, Ramin","last_name":"Golestanian","first_name":"Ramin"},{"last_name":"Isa","first_name":"Lucio","full_name":"Isa, Lucio"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"last_name":"Löwen","first_name":"Hartmut","full_name":"Löwen, Hartmut"},{"full_name":"Metzler, Ralf","last_name":"Metzler","first_name":"Ralf"},{"full_name":"Polin, Marco","last_name":"Polin","first_name":"Marco"},{"last_name":"Royall","first_name":"C. Patrick","full_name":"Royall, C. Patrick"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Anupam","last_name":"Sengupta","full_name":"Sengupta, Anupam"},{"first_name":"Cécile","last_name":"Sykes","full_name":"Sykes, Cécile"},{"first_name":"Vito","last_name":"Trianni","full_name":"Trianni, Vito"},{"last_name":"Tuval","first_name":"Idan","full_name":"Tuval, Idan"},{"first_name":"Nicolas","last_name":"Vogel","full_name":"Vogel, Nicolas"},{"first_name":"Julia M.","last_name":"Yeomans","full_name":"Yeomans, Julia M."},{"first_name":"Iker","last_name":"Zuriguel","full_name":"Zuriguel, Iker"},{"full_name":"Marin, Alvaro","first_name":"Alvaro","last_name":"Marin"},{"full_name":"Volpe, Giorgio","last_name":"Volpe","first_name":"Giorgio"}],"volume":19,"date_updated":"2023-08-01T13:28:39Z","date_created":"2023-03-05T23:01:06Z","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","year":"2023","publisher":"Royal Society of Chemistry","department":[{"_id":"AnSa"}],"publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"month":"02","doi":"10.1039/d2sm01562e","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000940388100001"],"arxiv":["2204.10059"]},"oa":1,"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12711","relation":"main_file","success":1,"checksum":"af95aa18b9b01e32fb8f13477c0e2687","date_created":"2023-03-07T09:19:41Z","date_updated":"2023-03-07T09:19:41Z","access_level":"open_access","file_name":"2023_SoftMatter_Araujo.pdf","creator":"cchlebak","file_size":3581939,"content_type":"application/pdf"}],"_id":"12708","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 19","ddc":["540"],"title":"Steering self-organisation through confinement","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","date_published":"2023-02-06T00:00:00Z","citation":{"apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e."},"publication":"Soft Matter","page":"1695-1704","article_type":"original"},{"date_updated":"2023-08-01T13:36:11Z","date_created":"2023-03-05T23:01:04Z","volume":14,"author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"first_name":"Sebastien","last_name":"Hamel","full_name":"Hamel, Sebastien"},{"first_name":"Mandy","last_name":"Bethkenhagen","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BiCh"}],"acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","year":"2023","pmid":1,"file_date_updated":"2023-03-07T10:58:00Z","article_number":"1104","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-36841-1","quality_controlled":"1","isi":1,"project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000939678300002"],"pmid":["36843123"]},"month":"02","publication_identifier":{"eissn":["2041-1723"]},"file":[{"date_created":"2023-03-07T10:58:00Z","date_updated":"2023-03-07T10:58:00Z","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","file_id":"12713","relation":"main_file","creator":"cchlebak","file_size":1946443,"content_type":"application/pdf","file_name":"2023_NatComm_Cheng.pdf","access_level":"open_access"}],"oa_version":"Published Version","status":"public","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","ddc":["540"],"intvolume":" 14","_id":"12702","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.","lang":"eng"}],"type":"journal_article","date_published":"2023-02-27T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1."},"day":"27","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"type":"journal_article","abstract":[{"text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12719","intvolume":" 15","title":"Refining epigenetic prediction of chronological and biological age","ddc":["570"],"status":"public","file":[{"relation":"main_file","file_id":"12722","checksum":"833b837910c4db42fb5f0f34125f77a7","success":1,"date_updated":"2023-03-14T10:29:47Z","date_created":"2023-03-14T10:29:47Z","access_level":"open_access","file_name":"2023_GenomeMed_Bernabeu.pdf","file_size":4275987,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"28","citation":{"ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y."},"publication":"Genome Medicine","article_type":"original","date_published":"2023-02-28T00:00:00Z","article_number":"12","file_date_updated":"2023-03-14T10:29:47Z","acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","year":"2023","publisher":"Springer Nature","department":[{"_id":"MaRo"}],"publication_status":"published","author":[{"last_name":"Bernabeu","first_name":"Elena","full_name":"Bernabeu, Elena"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."},{"first_name":"Ake T.","last_name":"Lu","full_name":"Lu, Ake T."},{"last_name":"Murphy","first_name":"Lee","full_name":"Murphy, Lee"},{"full_name":"Wrobel, Nicola","first_name":"Nicola","last_name":"Wrobel"},{"first_name":"Archie","last_name":"Campbell","full_name":"Campbell, Archie"},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"full_name":"Liewald, David","first_name":"David","last_name":"Liewald"},{"last_name":"Hayward","first_name":"Caroline","full_name":"Hayward, Caroline"},{"first_name":"Cathie","last_name":"Sudlow","full_name":"Sudlow, Cathie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"full_name":"Horvath, Steve","first_name":"Steve","last_name":"Horvath"},{"last_name":"Mcintosh","first_name":"Andrew M.","full_name":"Mcintosh, Andrew M."},{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"last_name":"Vallejos","first_name":"Catalina A.","full_name":"Vallejos, Catalina A."},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."}],"volume":15,"date_created":"2023-03-12T23:01:02Z","date_updated":"2023-08-01T13:38:12Z","publication_identifier":{"eissn":["1756-994X"]},"month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000940286600001"]},"isi":1,"quality_controlled":"1","doi":"10.1186/s13073-023-01161-y","language":[{"iso":"eng"}]},{"citation":{"chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930"},"publication":"IEEE Robotics and Automation Letters","page":"1595-1602","article_type":"original","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","_id":"12704","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 8","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","status":"public","ddc":["000"],"file":[{"file_name":"2023_IEEERobAutLetters_Lechner.pdf","access_level":"open_access","file_size":944052,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"12714","date_created":"2023-03-07T12:22:23Z","date_updated":"2023-03-07T12:22:23Z","checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000936534100012"],"arxiv":["2204.07373"]},"isi":1,"quality_controlled":"1","doi":"10.1109/LRA.2023.3240930","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2377-3766"]},"month":"03","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","year":"2023","department":[{"_id":"ToHe"}],"publisher":"Institute of Electrical and Electronics Engineers","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"11366"}]},"author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"volume":8,"date_updated":"2023-08-01T13:36:50Z","date_created":"2023-03-05T23:01:04Z","file_date_updated":"2023-03-07T12:22:23Z"},{"external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"isi":1,"quality_controlled":"1","doi":"10.1021/acs.inorgchem.3c00057","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0020-1669"],"eissn":["1520-510X"]},"acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used.","year":"2023","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"StFr"}],"author":[{"full_name":"García-Romero, Álvaro","first_name":"Álvaro","last_name":"García-Romero"},{"full_name":"Waters, Jessica E.","last_name":"Waters","first_name":"Jessica E."},{"orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B"},{"full_name":"Bond, Andrew D.","first_name":"Andrew D.","last_name":"Bond"},{"first_name":"Annie L.","last_name":"Colebatch","full_name":"Colebatch, Annie L."},{"last_name":"García-Rodríguez","first_name":"Raúl","full_name":"García-Rodríguez, Raúl"},{"full_name":"Wright, Dominic S.","last_name":"Wright","first_name":"Dominic S."}],"date_created":"2023-03-19T23:00:59Z","date_updated":"2023-08-01T13:42:59Z","volume":62,"publication":"Inorganic Chemistry","citation":{"ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057","ieee":"Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057","chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057.","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636."},"article_type":"original","page":"4625-4636","date_published":"2023-03-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"No","_id":"12737","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","status":"public","intvolume":" 62","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed."}],"issue":"11"},{"oa_version":"Preprint","intvolume":" 130","title":"Spin-electric coupling in lead halide perovskites","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12723","issue":"10","abstract":[{"lang":"eng","text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order."}],"type":"journal_article","date_published":"2023-03-10T00:00:00Z","article_type":"original","citation":{"ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901."},"publication":"Physical Review Letters","article_processing_charge":"No","day":"10","keyword":["General Physics and Astronomy"],"scopus_import":"1","volume":130,"date_created":"2023-03-14T13:11:59Z","date_updated":"2023-08-01T13:39:04Z","author":[{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"},{"full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"full_name":"Lorenc, Dusan","first_name":"Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes","last_name":"Ashourishokri"},{"full_name":"Zhumekenov, Ayan A.","first_name":"Ayan A.","last_name":"Zhumekenov"},{"last_name":"Bakr","first_name":"Osman M.","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"}],"publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","year":"2023","article_number":"106901","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.106901","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.09443","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2203.09443"],"isi":["000982435900002"]},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03"},{"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.107.125201","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"oa":1,"external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"article_number":"125201","volume":107,"date_created":"2023-03-14T13:13:05Z","date_updated":"2023-08-01T13:39:47Z","author":[{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"},{"full_name":"Shiva Kumar, Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar"},{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"full_name":"Ashourishokri, Younes","last_name":"Ashourishokri","first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334"},{"last_name":"Zhumekenov","first_name":"Ayan","full_name":"Zhumekenov, Ayan"},{"last_name":"Bakr","first_name":"Osman M.","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"}],"publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","year":"2023","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2023-03-15T00:00:00Z","article_type":"original","citation":{"chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201.","ieee":"A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201"},"publication":"Physical Review B","issue":"12","abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 107","title":"Effective model for studying optical properties of lead halide perovskites","status":"public","_id":"12724","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"citation":{"short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148."},"publication":"PLoS ONE","article_type":"original","date_published":"2023-03-17T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"17","_id":"12759","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 18","status":"public","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","ddc":["570"],"file":[{"checksum":"2380331ec27cc87808826fc64419ac1c","success":1,"date_created":"2023-03-27T06:51:09Z","date_updated":"2023-03-27T06:51:09Z","relation":"main_file","file_id":"12770","content_type":"application/pdf","file_size":7290413,"creator":"dernst","access_level":"open_access","file_name":"2023_PLoSOne_Rothman.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"3 March","abstract":[{"text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density.","lang":"eng"}],"external_id":{"isi":["001024737400001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0277148","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"eissn":["1932-6203"]},"month":"03","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","year":"2023","department":[{"_id":"PeJo"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"full_name":"Rothman, Jason Seth","last_name":"Rothman","first_name":"Jason Seth"},{"last_name":"Borges Merjane","first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"full_name":"Holderith, Noemi","last_name":"Holderith","first_name":"Noemi"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"last_name":"Angus Silver","first_name":"R.","full_name":"Angus Silver, R."}],"volume":18,"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:46:39Z","article_number":"e0277148","ec_funded":1,"file_date_updated":"2023-03-27T06:51:09Z"},{"date_published":"2023-03-17T00:00:00Z","citation":{"ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","ieee":"F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224","ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023)."},"publication":"Science Advances","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2023-03-27T06:24:49Z","date_updated":"2023-03-27T06:24:49Z","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","file_id":"12768","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1826471,"file_name":"2023_ScienceAdvances_Hurtig.pdf","access_level":"open_access"}],"_id":"12756","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","status":"public","ddc":["570"],"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","issue":"11","abstract":[{"text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling.","lang":"eng"}],"type":"journal_article","doi":"10.1126/sciadv.ade5224","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000968083500010"]},"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2375-2548"]},"month":"03","author":[{"last_name":"Hurtig","first_name":"Fredrik","full_name":"Hurtig, Fredrik"},{"first_name":"Thomas C.Q.","last_name":"Burgers","full_name":"Burgers, Thomas C.Q."},{"full_name":"Cezanne, Alice","last_name":"Cezanne","first_name":"Alice"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"full_name":"Mol, Frank N.","first_name":"Frank N.","last_name":"Mol"},{"last_name":"Traparić","first_name":"Jovan","full_name":"Traparić, Jovan"},{"last_name":"Pulschen","first_name":"Andre Arashiro","full_name":"Pulschen, Andre Arashiro"},{"first_name":"Tim","last_name":"Nierhaus","full_name":"Nierhaus, Tim"},{"first_name":"Gabriel","last_name":"Tarrason-Risa","full_name":"Tarrason-Risa, Gabriel"},{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"last_name":"Löwe","first_name":"Jan","full_name":"Löwe, Jan"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Vlijm, Rifka","first_name":"Rifka","last_name":"Vlijm"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"}],"volume":9,"date_updated":"2023-08-01T13:45:54Z","date_created":"2023-03-26T22:01:06Z","year":"2023","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","publisher":"American Association for the Advancement of Science","department":[{"_id":"AnSa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-03-27T06:24:49Z","article_number":"eade5224"},{"intvolume":" 18","ddc":["570"],"status":"public","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","_id":"12758","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"date_updated":"2023-03-27T07:09:08Z","date_created":"2023-03-27T07:09:08Z","success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","file_id":"12771","relation":"main_file","creator":"dernst","file_size":856625,"content_type":"application/pdf","file_name":"2023_PLoSOne_Pak.pdf","access_level":"open_access"}],"type":"journal_article","issue":"3","abstract":[{"text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding.","lang":"eng"}],"article_type":"original","citation":{"chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","ieee":"M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689"},"publication":"PLoS ONE","date_published":"2023-03-16T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"16","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2023","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","volume":18,"date_updated":"2023-08-01T13:47:14Z","date_created":"2023-03-26T22:01:07Z","author":[{"first_name":"Marina A.","last_name":"Pak","full_name":"Pak, Marina A."},{"last_name":"Markhieva","first_name":"Karina A.","full_name":"Markhieva, Karina A."},{"full_name":"Novikova, Mariia S.","last_name":"Novikova","first_name":"Mariia S."},{"last_name":"Petrov","first_name":"Dmitry S.","full_name":"Petrov, Dmitry S."},{"first_name":"Ilya S.","last_name":"Vorobyev","full_name":"Vorobyev, Ilya S."},{"full_name":"Maksimova, Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","last_name":"Maksimova","first_name":"Ekaterina"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N.","last_name":"Ivankov","first_name":"Dmitry N."}],"article_number":"e0282689","file_date_updated":"2023-03-27T07:09:08Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000985134400106"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0282689","publication_identifier":{"eissn":["1932-6203"]},"month":"03"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15","page":"319-333","article_type":"review","citation":{"ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285."},"publication":"The Biochemical Journal","date_published":"2023-03-15T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.","lang":"eng"}],"intvolume":" 480","ddc":["570"],"title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12757","oa_version":"Published Version","publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"month":"03","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1042/BCJ20210285"}],"external_id":{"pmid":["36920092"],"isi":["000957065700001"]},"language":[{"iso":"eng"}],"doi":"10.1042/BCJ20210285","publisher":"Portland Press","department":[{"_id":"LeSa"}],"publication_status":"published","pmid":1,"year":"2023","volume":480,"date_created":"2023-03-26T22:01:06Z","date_updated":"2023-08-01T13:45:12Z","author":[{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}]},{"year":"2023","acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","publication_status":"published","publisher":"The Royal Society","department":[{"_id":"KrCh"}],"author":[{"full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"last_name":"Kaveh","first_name":"Kamran","full_name":"Kaveh, Kamran"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}],"related_material":{"link":[{"relation":"research_data","url":"https://doi.org/10.6084/m9.figshare.21261771.v1"}]},"date_created":"2023-04-02T22:01:09Z","date_updated":"2023-08-01T13:58:34Z","volume":479,"article_number":"20220685","file_date_updated":"2023-04-03T06:25:29Z","ec_funded":1,"external_id":{"isi":["000957125500002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"doi":"10.1098/rspa.2022.0685","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["1364-5021"],"eissn":["1471-2946"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12787","ddc":["000"],"status":"public","title":"Coexistence times in the Moran process with environmental heterogeneity","intvolume":" 479","oa_version":"Published Version","file":[{"file_id":"12796","relation":"main_file","success":1,"checksum":"13953d349fbefcb5d21ccc6b303297eb","date_updated":"2023-04-03T06:25:29Z","date_created":"2023-04-03T06:25:29Z","access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","creator":"dernst","file_size":827784,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results.","lang":"eng"}],"issue":"2271","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.","ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685"},"article_type":"original","date_published":"2023-03-29T00:00:00Z","scopus_import":"1","day":"29","has_accepted_license":"1","article_processing_charge":"No"},{"title":"Topological charges of periodically kicked molecules","status":"public","intvolume":" 130","_id":"12788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}],"issue":"10","article_type":"original","publication":"Physical Review Letters","citation":{"ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202."},"date_published":"2023-03-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"year":"2023","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T14:02:06Z","volume":130,"author":[{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","last_name":"Karle","full_name":"Karle, Volker"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/","relation":"press_release","description":"News on the ISTA website"}]},"article_number":"103202","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.07067","open_access":"1"}],"external_id":{"arxiv":["2206.07067"],"isi":["000957635500003"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.130.103202","month":"03","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]}},{"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"Physical Review B","citation":{"chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.","apa":"Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502","ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023.","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502"},"date_published":"2023-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity.","lang":"eng"}],"issue":"10","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","status":"public","intvolume":" 107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12790","oa_version":"Preprint","month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.02492","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.107.104502","article_number":"104502","publication_status":"published","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publisher":"American Physical Society","acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","year":"2023","date_updated":"2023-08-01T13:59:29Z","date_created":"2023-04-02T22:01:10Z","volume":107,"author":[{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"full_name":"Holder, Tobias","last_name":"Holder","first_name":"Tobias"},{"last_name":"Berg","first_name":"Erez","full_name":"Berg, Erez"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"related_material":{"link":[{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/"}]}},{"publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"month":"03","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2301.07769"}],"external_id":{"isi":["000956387200001"],"arxiv":["2301.07769"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1140/epje/s10189-023-00276-9","language":[{"iso":"eng"}],"article_number":"16","year":"2023","acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Clark Di Leoni, Patricio","last_name":"Clark Di Leoni","first_name":"Patricio"},{"id":"cd100965-0804-11ed-9c55-f4878ff4e877","first_name":"Lokahith N","last_name":"Agasthya","full_name":"Agasthya, Lokahith N"},{"last_name":"Buzzicotti","first_name":"Michele","full_name":"Buzzicotti, Michele"},{"full_name":"Biferale, Luca","last_name":"Biferale","first_name":"Luca"}],"volume":46,"date_updated":"2023-08-01T14:03:47Z","date_created":"2023-04-02T22:01:11Z","scopus_import":"1","article_processing_charge":"No","day":"20","citation":{"apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9","ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023.","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9","chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9."},"publication":"The European Physical Journal E","article_type":"original","date_published":"2023-03-20T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12791","intvolume":" 46","status":"public","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","oa_version":"Preprint"},{"date_published":"2023-04-10T00:00:00Z","page":"582-596.e7","article_type":"original","citation":{"apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016."},"publication":"Developmental Cell","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"10","scopus_import":"1","file":[{"file_id":"12842","relation":"main_file","date_created":"2023-04-17T07:41:25Z","date_updated":"2023-04-17T07:41:25Z","success":1,"checksum":"c80ca2ebc241232aacdb5aa4b4c80957","file_name":"2023_DevelopmentalCell_Huljev.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":7925886}],"oa_version":"Published Version","intvolume":" 58","ddc":["570"],"status":"public","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","_id":"12830","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"doi":"10.1016/j.devcel.2023.02.016","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation"},{"grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000982111800001"]},"oa":1,"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"month":"04","volume":58,"date_updated":"2023-08-01T14:10:38Z","date_created":"2023-04-16T22:01:07Z","author":[{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"full_name":"Nunes Pinheiro, Diana C","last_name":"Nunes Pinheiro","first_name":"Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Preusser","first_name":"Friedrich","full_name":"Preusser, Friedrich"},{"full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","first_name":"Irene"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"full_name":"Naik, Suyash","orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","last_name":"Naik","first_name":"Suyash"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication_status":"published","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","year":"2023","ec_funded":1,"file_date_updated":"2023-04-17T07:41:25Z"}]