[{"month":"01","publication_identifier":{"issn":["1553-7374"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1371/journal.ppat.1008277","isi":1,"quality_controlled":"1","project":[{"grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:59Z","article_number":"e1008277","date_updated":"2023-10-17T12:29:34Z","date_created":"2020-02-06T18:47:17Z","volume":16,"author":[{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"first_name":"Dustin R.","last_name":"Morado","full_name":"Morado, Dustin R."},{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","first_name":"Vladyslav"},{"full_name":"Ricana, Clifton L.","first_name":"Clifton L.","last_name":"Ricana"},{"last_name":"Lyddon","first_name":"Terri D.","full_name":"Lyddon, Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"full_name":"Feathers, J. Ryan","first_name":"J. Ryan","last_name":"Feathers"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"last_name":"Perilla","first_name":"Juan R.","full_name":"Perilla, Juan R."},{"full_name":"Briggs, John A. G.","first_name":"John A. G.","last_name":"Briggs"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"related_material":{"record":[{"status":"deleted","relation":"research_data","id":"9723"}]},"publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Public Library of Science","year":"2020","pmid":1,"day":"27","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-01-27T00:00:00Z","article_type":"original","publication":"PLOS Pathogens","citation":{"chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277"},"abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_PLOSPatho_Dick.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4551246,"creator":"dernst","relation":"main_file","file_id":"7484","date_created":"2020-02-11T10:07:28Z","date_updated":"2020-07-14T12:47:59Z","checksum":"a297f54d1fef0efe4789ca00f37f241e"}],"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","ddc":["570"],"status":"public","intvolume":" 16","_id":"7464","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ddc":["000"],"status":"public","title":"Limits on amplifiers of natural selection under death-Birth updating","intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7212","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1817531,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_PlosCompBio_Tkadlec.pdf","checksum":"ce32ee2d2f53aed832f78bbd47e882df","date_updated":"2020-07-14T12:47:53Z","date_created":"2020-02-03T07:32:42Z","file_id":"7441","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process."}],"article_type":"original","publication":"PLoS computational biology","citation":{"ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494.","mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020)."},"date_published":"2020-01-17T00:00:00Z","scopus_import":"1","day":"17","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"year":"2020","date_updated":"2023-10-17T12:29:47Z","date_created":"2019-12-23T13:45:11Z","volume":16,"author":[{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7196"}]},"article_number":"e1007494","file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"external_id":{"isi":["000510916500025"],"arxiv":["1906.02785"]},"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":"10.1371/journal.pcbi.1007494","month":"01","publication_identifier":{"eissn":["15537358"]}},{"_id":"7196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A role of graphs in evolutionary processes","status":"public","ddc":["519"],"file":[{"date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-12T11:49:49Z","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","relation":"source_file","file_id":"7255","content_type":"application/zip","file_size":21100497,"creator":"jtkadlec","file_name":"thesis.zip","access_level":"closed"},{"checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-28T07:32:42Z","file_id":"7367","relation":"main_file","creator":"dernst","file_size":11670983,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Tkadlec_Thesis.pdf"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"citation":{"short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria."},"page":"144","date_published":"2020-01-12T00:00:00Z","day":"12","article_processing_charge":"No","has_accepted_license":"1","year":"2020","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"}],"related_material":{"record":[{"id":"7210","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5751"},{"id":"7212","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-10-17T12:29:46Z","date_created":"2019-12-20T12:26:36Z","file_date_updated":"2020-07-14T12:47:52Z","oa":1,"doi":"10.15479/AT:ISTA:7196","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["2663-337X"]}},{"date_published":"2020-07-13T00:00:00Z","page":"8773-8784","citation":{"ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84."},"publication":"Proceedings of the 37th International Conference on Machine Learning","article_processing_charge":"No","has_accepted_license":"1","day":"13","file":[{"access_level":"open_access","file_name":"2020_PMLR_Shevchenko.pdf","content_type":"application/pdf","file_size":5336380,"creator":"dernst","relation":"main_file","file_id":"9217","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","success":1,"date_updated":"2021-03-02T15:38:14Z","date_created":"2021-03-02T15:38:14Z"}],"oa_version":"Published Version","intvolume":" 119","title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","ddc":["000"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9198","abstract":[{"text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1912.10095"]},"month":"07","volume":119,"date_created":"2021-02-25T09:36:22Z","date_updated":"2023-10-17T12:43:19Z","author":[{"full_name":"Shevchenko, Alexander","last_name":"Shevchenko","first_name":"Alexander"},{"full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020"}],"department":[{"_id":"MaMo"}],"publisher":"ML Research Press","publication_status":"published","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","year":"2020","file_date_updated":"2021-03-02T15:38:14Z"},{"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"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"}],"doi":"10.1515/cmb-2020-0100","publication_identifier":{"issn":["2544-7297"]},"month":"06","publisher":"De Gruyter","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","volume":8,"date_updated":"2023-10-17T12:34:51Z","date_created":"2021-02-17T15:13:01Z","author":[{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"ec_funded":1,"file_date_updated":"2021-02-19T13:56:24Z","page":"51-67","article_type":"original","citation":{"chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100"},"publication":"Computational and Mathematical Biophysics","date_published":"2020-06-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"20","intvolume":" 8","title":"The weighted mean curvature derivative of a space-filling diagram","status":"public","ddc":["510"],"_id":"9157","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"9171","relation":"main_file","success":1,"checksum":"cea41de9937d07a3b927d71ee8b4e432","date_created":"2021-02-19T13:56:24Z","date_updated":"2021-02-19T13:56:24Z","access_level":"open_access","file_name":"2020_CompMathBiophysics_Akopyan2.pdf","creator":"dernst","file_size":562359,"content_type":"application/pdf"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}]},{"file":[{"file_name":"2020_CompMathBiophysics_Akopyan.pdf","access_level":"open_access","creator":"dernst","file_size":707452,"content_type":"application/pdf","file_id":"9170","relation":"main_file","date_updated":"2021-02-19T13:33:19Z","date_created":"2021-02-19T13:33:19Z","success":1,"checksum":"ca43a7440834eab6bbea29c59b56ef3a"}],"oa_version":"Published Version","status":"public","ddc":["510"],"title":"The weighted Gaussian curvature derivative of a space-filling diagram","intvolume":" 8","_id":"9156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2020-07-21T00:00:00Z","article_type":"original","page":"74-88","publication":"Computational and Mathematical Biophysics","citation":{"chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101"},"day":"21","article_processing_charge":"No","has_accepted_license":"1","date_created":"2021-02-17T15:12:44Z","date_updated":"2023-10-17T12:35:10Z","volume":8,"author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"De Gruyter","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","file_date_updated":"2021-02-19T13:33:19Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1515/cmb-2020-0101","quality_controlled":"1","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"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":["1908.06777"]},"oa":1,"month":"07","publication_identifier":{"issn":["2544-7297"]}},{"file":[{"file_id":"8976","relation":"main_file","date_updated":"2020-12-28T08:24:08Z","date_created":"2020-12-28T08:24:08Z","success":1,"checksum":"d75359b9814e78d57c0a481b7cde3751","file_name":"2020_ElectronJProbab_Redig.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":696653}],"oa_version":"Published Version","_id":"8973","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 25","status":"public","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","ddc":["510"],"abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"type":"journal_article","date_published":"2020-10-21T00:00:00Z","citation":{"ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020)."},"publication":"Electronic Journal of Probability","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"21","scopus_import":"1","author":[{"first_name":"Frank","last_name":"Redig","full_name":"Redig, Frank"},{"last_name":"Saada","first_name":"Ellen","full_name":"Saada, Ellen"},{"id":"E1836206-9F16-11E9-8814-AEFDE5697425","last_name":"Sau","first_name":"Federico","full_name":"Sau, Federico"}],"volume":25,"date_updated":"2023-10-17T12:51:56Z","date_created":"2020-12-27T23:01:17Z","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","year":"2020","publisher":" Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-12-28T08:24:08Z","article_number":"138","doi":"10.1214/20-EJP536","language":[{"iso":"eng"}],"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1083-6489"]},"month":"10"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"179","intvolume":" 169","title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","status":"public","oa_version":"Preprint","type":"journal_article","issue":"16","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.","lang":"eng"}],"citation":{"short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal. Duke University Press, 2020. https://doi.org/10.1215/00127094-2020-0031.","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 2020;169(16):3099-3165. doi:10.1215/00127094-2020-0031","apa":"Browning, T. D., & Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2020-0031","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” Duke Mathematical Journal, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165."},"publication":"Duke Mathematical Journal","page":"3099-3165","article_type":"original","date_published":"2020-09-10T00:00:00Z","article_processing_charge":"No","day":"10","year":"2020","department":[{"_id":"TiBr"}],"publisher":"Duke University Press","publication_status":"published","author":[{"full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heath Brown, Roger","first_name":"Roger","last_name":"Heath Brown"}],"volume":169,"date_updated":"2023-10-17T12:51:10Z","date_created":"2018-12-11T11:45:02Z","external_id":{"arxiv":["1805.10715"],"isi":["000582676300002"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"quality_controlled":"1","isi":1,"doi":"10.1215/00127094-2020-0031","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-7094"]},"month":"09"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners"}],"department":[{"_id":"KrCh"}],"publisher":"Royal Society","status":"public","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","_id":"9814","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","oa_version":"Published Version","date_updated":"2023-10-18T06:36:00Z","date_created":"2021-08-06T13:09:57Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"198"}]},"author":[{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"article_processing_charge":"No","day":"15","month":"10","citation":{"short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","mla":"Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1.","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, 10.6084/m9.figshare.5973013.v1."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"doi":"10.6084/m9.figshare.5973013.v1","date_published":"2020-10-15T00:00:00Z"},{"abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"issue":"4","type":"journal_article","oa_version":"Preprint","_id":"8285","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","status":"public","intvolume":" 125","day":"24","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-24T00:00:00Z","publication":"Physical Review Letters","citation":{"ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202.","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020)."},"article_type":"original","article_number":"043202","author":[{"full_name":"Malia, Benjamin K.","first_name":"Benjamin K.","last_name":"Malia"},{"first_name":"Julián","last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián"},{"last_name":"Wu","first_name":"Yunfan","full_name":"Wu, Yunfan"},{"orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur","full_name":"Hosten, Onur"},{"first_name":"Mark A.","last_name":"Kasevich","full_name":"Kasevich, Mark A."}],"date_created":"2020-08-24T06:24:04Z","date_updated":"2023-10-18T08:38:35Z","volume":125,"year":"2020","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","pmid":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"OnHo"}],"month":"07","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/PhysRevLett.125.043202","language":[{"iso":"eng"}],"external_id":{"pmid":["32794788"],"isi":["000552227400008"],"arxiv":["1912.10218"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"oa":1,"isi":1,"quality_controlled":"1"},{"date_published":"2020-01-01T00:00:00Z","doi":"10.1364/QUANTUM.2020.QTu8A.1","conference":{"start_date":"2020-09-14","location":"Washington, DC, United States","end_date":"2020-09-17","name":"OSA: Optical Society of America"},"language":[{"iso":"eng"}],"citation":{"chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1.","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1","ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1"},"publication":"OSA Quantum 2.0 Conference","quality_controlled":"1","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"article_processing_charge":"No","day":"01","month":"01","scopus_import":"1","author":[{"first_name":"Nicholas J.","last_name":"Lambert","full_name":"Lambert, Nicholas J."},{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"oa_version":"None","date_updated":"2023-10-18T08:32:34Z","date_created":"2021-11-21T23:01:31Z","_id":"10328","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"title":"New designs and noise channels in electro-optic microwave to optical up-conversion","publication_status":"published","status":"public","abstract":[{"text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient.","lang":"eng"}],"type":"conference","article_number":"QTu8A.1","alternative_title":["OSA Technical Digest"]},{"month":"12","publication_identifier":{"issn":["1049-5258"]},"quality_controlled":"1","project":[{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z"},{"grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020"}],"main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2020-12-12","location":"Vancouver, Canada","start_date":"2020-12-06","name":"NeurIPS: Conference on Neural Information Processing Systems"},"ec_funded":1,"publication_status":"published","department":[{"_id":"TiVo"}],"year":"2020","acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","date_updated":"2023-10-18T09:20:55Z","date_created":"2021-07-04T22:01:27Z","volume":33,"author":[{"first_name":"Basile J","last_name":"Confavreux","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"},{"last_name":"Agnes","first_name":"Everton J.","full_name":"Agnes, Everton J."},{"last_name":"Lillicrap","first_name":"Timothy","full_name":"Lillicrap, Timothy"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14422"}],"link":[{"relation":"is_continued_by","url":"https://doi.org/10.1101/2020.10.24.353409"}]},"scopus_import":"1","day":"06","article_processing_charge":"No","page":"16398-16408","publication":"Advances in Neural Information Processing Systems","citation":{"mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada."},"date_published":"2020-12-06T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","status":"public","intvolume":" 33","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9633","oa_version":"Published Version"},{"publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","year":"2020","volume":33,"date_created":"2020-12-13T23:01:21Z","date_updated":"2023-11-16T13:03:31Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/plants-on-aspirin/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"full_name":"Liu, Jie","first_name":"Jie","last_name":"Liu"},{"last_name":"Bailly","first_name":"Aurélien","full_name":"Bailly, Aurélien"},{"last_name":"Ferro","first_name":"Noel","full_name":"Ferro, Noel"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"article_number":"108463","ec_funded":1,"file_date_updated":"2020-12-14T07:33:39Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"}],"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":["000595658100018"],"pmid":["33264621"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1016/j.celrep.2020.108463","publication_identifier":{"eissn":["22111247"]},"month":"12","intvolume":" 33","ddc":["580"],"title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","status":"public","_id":"8943","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"success":1,"checksum":"ed18cba0fb48ed2e789381a54cc21904","date_updated":"2020-12-14T07:33:39Z","date_created":"2020-12-14T07:33:39Z","file_id":"8948","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":8056434,"access_level":"open_access","file_name":"2020_CellReports_Tan.pdf"}],"type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"article_type":"original","citation":{"ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463","ieee":"S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020.","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463.","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463."},"publication":"Cell Reports","date_published":"2020-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01"},{"author":[{"id":"3454D55E-F248-11E8-B48F-1D18A9856A87","first_name":"Duo","last_name":"Xu","full_name":"Xu, Duo"},{"full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ma, Xingyu","first_name":"Xingyu","last_name":"Ma","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0179-9737"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"first_name":"Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"12726","relation":"dissertation_contains","status":"public"},{"id":"14530","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-11-30T10:55:13Z","date_created":"2020-06-07T22:00:51Z","volume":117,"year":"2020","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","ec_funded":1,"doi":"10.1073/pnas.1913716117","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2005.11190","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"]},"quality_controlled":"1","isi":1,"project":[{"name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF","grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"month":"05","publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"oa_version":"Preprint","_id":"7932","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","intvolume":" 117","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"issue":"21","type":"journal_article","date_published":"2020-05-26T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117."},"article_type":"original","page":"11233-11239","day":"26","article_processing_charge":"No","scopus_import":"1"},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"01","keyword":["General Mathematics"],"date_published":"2020-09-01T00:00:00Z","citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539."},"publication":"Documenta Mathematica","page":"1421-1539","article_type":"original","abstract":[{"text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases.","lang":"eng"}],"type":"journal_article","file":[{"checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","success":1,"date_created":"2023-12-18T10:42:32Z","date_updated":"2023-12-18T10:42:32Z","relation":"main_file","file_id":"14695","file_size":1374708,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_DocumentaMathematica_Alt.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14694","intvolume":" 25","ddc":["510"],"status":"public","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"month":"09","doi":"10.4171/dm/780","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":{"arxiv":["1804.07752"]},"quality_controlled":"1","file_date_updated":"2023-12-18T10:42:32Z","related_material":{"record":[{"id":"6183","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"volume":25,"date_updated":"2023-12-18T10:46:09Z","date_created":"2023-12-18T10:37:43Z","year":"2020","publisher":"EMS Press","department":[{"_id":"LaEr"}],"publication_status":"published"},{"page":"119","citation":{"ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156."},"date_published":"2020-07-24T00:00:00Z","day":"24","has_accepted_license":"1","article_processing_charge":"No","title":"Topological methods in geometry and discrete mathematics","ddc":["514"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8156","oa_version":"Published Version","file":[{"creator":"savvakum","content_type":"application/zip","file_size":1061740,"file_name":"source.zip","access_level":"closed","date_created":"2020-07-27T12:44:51Z","date_updated":"2020-07-27T12:44:51Z","file_id":"8178","relation":"source_file"},{"access_level":"open_access","file_name":"thesis_pdfa.pdf","file_size":1336501,"content_type":"application/pdf","creator":"savvakum","relation":"main_file","file_id":"8179","success":1,"date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-27T12:46:53Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. 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We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space."}],"citation":{"mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis. 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Sweeney, Neuroscience 450 (2020) 81–95."},"date_published":"2020-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord."}],"status":"public","ddc":["570"],"title":"Differential loss of spinal interneurons in a mouse model of ALS","intvolume":" 450","_id":"8914","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_Neuroscience_Salamatina.pdf","content_type":"application/pdf","file_size":4071247,"creator":"dernst","relation":"main_file","file_id":"8915","checksum":"da7413c819e079720669c82451b49294","success":1,"date_updated":"2020-12-03T11:45:26Z","date_created":"2020-12-03T11:45:26Z"}],"month":"12","publication_identifier":{"issn":["0306-4522"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000595588700008"],"pmid":["32858144"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.neuroscience.2020.08.011","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-12-03T11:45:26Z","publication_status":"published","department":[{"_id":"LoSw"}],"publisher":"Elsevier","acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. 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Arathoon, (2020)."},"date_published":"2020-08-18T00:00:00Z","doi":"10.15479/AT:ISTA:8254","article_processing_charge":"No","has_accepted_license":"1","month":"08","day":"18","_id":"8254","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"status":"public","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","related_material":{"record":[{"id":"11321","status":"public","relation":"later_version"},{"id":"9192","status":"public","relation":"later_version"}]},"contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","last_name":"Arathoon","first_name":"Louise S"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh","first_name":"Parvathy"},{"last_name":"Barton","contributor_type":"project_member","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","contributor_type":"project_member"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Pickup","first_name":"Melinda"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","contributor_type":"project_member"}],"author":[{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S"}],"oa_version":"Published Version","file":[{"file_name":"Data_Rcode_MathematicaNB.zip","access_level":"open_access","content_type":"application/x-zip-compressed","file_size":5778420,"creator":"dernst","relation":"main_file","file_id":"8280","date_created":"2020-08-18T08:03:23Z","date_updated":"2020-08-18T08:03:23Z","checksum":"4f1382ed4384751b6013398c11557bf6","success":1}],"date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","type":"research_data","file_date_updated":"2020-08-18T08:03:23Z","abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}]},{"article_type":"original","citation":{"apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523","ieee":"F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley, 2020.","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16). doi:10.1002/adma.201906523","chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523, Wiley, 2020, doi:10.1002/adma.201906523."},"publication":"Advanced Materials","date_published":"2020-04-23T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"23","intvolume":" 32","title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","status":"public","ddc":["530"],"_id":"7541","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"checksum":"c622737dc295972065782558337124a2","success":1,"date_updated":"2020-11-20T10:11:35Z","date_created":"2020-11-20T10:11:35Z","relation":"main_file","file_id":"8782","file_size":5242880,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_AdvancedMaterials_Gao.pdf"}],"type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon."}],"project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497"},{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020"}],"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":["000516660900001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"doi":"10.1002/adma.201906523","publication_identifier":{"issn":["0935-9648"]},"month":"04","department":[{"_id":"GeKa"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","year":"2020","volume":32,"date_created":"2020-02-28T09:47:00Z","date_updated":"2024-02-21T12:42:12Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7996"},{"status":"public","relation":"research_data","id":"9222"}]},"author":[{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"last_name":"Wang","first_name":"Jian-Huan","full_name":"Wang, Jian-Huan"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hao","last_name":"Hu","full_name":"Hu, Hao"},{"full_name":"Rančić, Marko J.","first_name":"Marko J.","last_name":"Rančić"},{"last_name":"Zhang","first_name":"Jie-Yin","full_name":"Zhang, Jie-Yin"},{"full_name":"Wang, Ting","first_name":"Ting","last_name":"Wang"},{"last_name":"Yao","first_name":"Yuan","full_name":"Yao, Yuan"},{"full_name":"Wang, Gui-Lei","first_name":"Gui-Lei","last_name":"Wang"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vukušić","first_name":"Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukušić, Lada"},{"full_name":"Kloeffel, Christoph","first_name":"Christoph","last_name":"Kloeffel"},{"full_name":"Loss, Daniel","last_name":"Loss","first_name":"Daniel"},{"full_name":"Liu, Feng","first_name":"Feng","last_name":"Liu"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"},{"last_name":"Zhang","first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun"}],"article_number":"1906523","ec_funded":1,"file_date_updated":"2020-11-20T10:11:35Z"},{"contributor":[{"first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"contributor_type":"supervisor","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8997","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"file":[{"access_level":"open_access","file_name":"PLoSCompBiol2020_datarep.zip","creator":"bkavcic","file_size":315494370,"content_type":"application/zip","file_id":"8932","relation":"main_file","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","date_created":"2020-12-09T15:00:19Z","date_updated":"2020-12-09T15:00:19Z"}],"oa_version":"Published Version","date_created":"2020-12-09T15:04:02Z","date_updated":"2024-02-21T12:41:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8930","year":"2020","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","status":"public","ddc":["570"],"file_date_updated":"2020-12-09T15:00:19Z","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"type":"research_data","date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930","citation":{"chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","short":"B. Kavcic, (2020).","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930"},"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,"has_accepted_license":"1","article_processing_charge":"No","day":"10","month":"12","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"]},{"abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"file_date_updated":"2020-12-20T22:01:44Z","type":"research_data","oa_version":"Published Version","file":[{"file_name":"readme.txt","access_level":"open_access","content_type":"text/plain","file_size":523,"creator":"bkavcic","relation":"main_file","file_id":"8952","date_created":"2020-12-20T09:52:52Z","date_updated":"2020-12-20T09:52:52Z","checksum":"f57862aeee1690c7effd2b1117d40ed1","success":1},{"checksum":"f2c6d5232ec6d551b6993991e8689e9f","success":1,"date_created":"2020-12-20T22:01:44Z","date_updated":"2020-12-20T22:01:44Z","relation":"main_file","file_id":"8954","file_size":379228,"content_type":"application/octet-stream","creator":"bkavcic","access_level":"open_access","file_name":"GRNs Research depository.gb"}],"date_created":"2020-12-20T10:00:26Z","date_updated":"2024-02-21T12:41:57Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9283"}]},"contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","contributor_type":"project_member","first_name":"Anna A"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","contributor_type":"project_member"},{"first_name":"Caroline","last_name":"Caruso Carter","contributor_type":"project_member"},{"last_name":"Sonnleitner","contributor_type":"project_member","first_name":"Elisabeth"},{"contributor_type":"project_member","last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixão","contributor_type":"project_member","first_name":"Tiago"},{"first_name":"Calin C","last_name":"Guet","contributor_type":"project_manager","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"author":[{"orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","first_name":"Anna A","full_name":"Nagy-Staron, Anna A"}],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","year":"2020","_id":"8951","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","has_accepted_license":"1","day":"21","month":"12","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8951","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"},"citation":{"ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020).","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951."}},{"day":"28","month":"01","has_accepted_license":"1","article_processing_charge":"No","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"doi":"10.15479/AT:ISTA:7383","date_published":"2020-01-28T00:00:00Z","oa":1,"citation":{"ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383."},"file_date_updated":"2020-07-14T12:47:57Z","abstract":[{"lang":"eng","text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"type":"research_data","author":[{"first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}],"contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","contributor_type":"project_leader"}],"related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"date_updated":"2024-02-21T12:42:31Z","date_created":"2020-01-28T10:41:49Z","file":[{"content_type":"application/zip","file_size":73363365,"creator":"rgrah","file_name":"Scripts.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:40Z","checksum":"9d292cf5207b3829225f44c044cdb3fd","relation":"main_file","file_id":"7384"},{"checksum":"4076ceab32ef588cc233802bab24c1ab","date_created":"2020-01-28T10:39:30Z","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","file_id":"7385","file_size":962,"content_type":"text/plain","creator":"rgrah","access_level":"open_access","file_name":"READ_ME_MAIN.txt"}],"oa_version":"Published Version","_id":"7383","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","status":"public","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria"},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222","chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","short":"G. Katsaros, (2020)."},"oa":1,"doi":"10.15479/AT:ISTA:9222","date_published":"2020-03-16T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","month":"03","day":"16","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["530"],"title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","year":"2020","_id":"9222","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"DOI_SiteControlledHWs.zip","creator":"gkatsaro","content_type":"application/x-zip-compressed","file_size":13317557,"file_id":"9223","relation":"main_file","checksum":"41b66e195ed3dbd73077feee77b05652","date_updated":"2021-03-05T17:50:45Z","date_created":"2021-03-05T17:50:45Z"},{"checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","success":1,"date_updated":"2021-03-10T07:31:50Z","date_created":"2021-03-10T07:31:50Z","relation":"main_file","file_id":"9233","file_size":3515,"content_type":"text/plain","creator":"dernst","access_level":"open_access","file_name":"Readme.txt"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:42:13Z","date_created":"2021-03-05T18:00:47Z","related_material":{"record":[{"id":"7541","relation":"used_in_publication","status":"public"}]},"contributor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","contributor_type":"research_group","last_name":"Katsaros"}],"author":[{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","file_date_updated":"2021-03-10T07:31:50Z"},{"day":"21","article_processing_charge":"No","has_accepted_license":"1","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"date_published":"2020-09-21T00:00:00Z","citation":{"ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366."},"page":"118","abstract":[{"lang":"eng","text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"access_level":"open_access","file_name":"thesis_rguseinov.pdf","creator":"rguseino","content_type":"application/pdf","file_size":70950442,"file_id":"8367","relation":"main_file","success":1,"checksum":"f8da89553da36037296b0a80f14ebf50","date_updated":"2020-09-10T16:11:49Z","date_created":"2020-09-10T16:11:49Z"},{"access_level":"closed","file_name":"thesis_source.zip","creator":"rguseino","file_size":76207597,"content_type":"application/x-zip-compressed","file_id":"8374","relation":"source_file","checksum":"e8fd944c960c20e0e27e6548af69121d","date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-11T09:39:48Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8366","ddc":["000"],"title":"Computational design of curved thin shells: From glass façades to programmable matter","status":"public","month":"09","publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8366","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"file_date_updated":"2020-09-16T15:11:01Z","ec_funded":1,"author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"research_data","status":"deleted","id":"7151"},{"id":"7262","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8562"},{"status":"public","relation":"part_of_dissertation","id":"1001"},{"relation":"research_data","status":"public","id":"8375"}]},"date_created":"2020-09-10T16:19:55Z","date_updated":"2024-02-21T12:44:29Z","year":"2020","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}]},{"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000595589100048"],"arxiv":["2009.03667"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3414685.3417843","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"month":"11","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2020","acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","volume":39,"date_created":"2020-09-23T11:30:02Z","date_updated":"2024-02-21T12:43:21Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/bend-dont-break/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8366"},{"status":"public","relation":"research_data","id":"8761"}]},"author":[{"full_name":"Gavriil, Konstantinos","first_name":"Konstantinos","last_name":"Gavriil"},{"full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","last_name":"Guseinov"},{"last_name":"Perez Rodriguez","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus"},{"first_name":"Davide","last_name":"Pellis","full_name":"Pellis, Davide"},{"full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","first_name":"Paul M","last_name":"Henderson"},{"first_name":"Florian","last_name":"Rist","full_name":"Rist, Florian"},{"full_name":"Pottmann, Helmut","last_name":"Pottmann","first_name":"Helmut"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"article_number":"208","ec_funded":1,"file_date_updated":"2023-05-23T20:54:43Z","article_type":"original","citation":{"chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3414685.3417843.","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:10.1145/3414685.3417843.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","ieee":"K. Gavriil et al., “Computational design of cold bent glass façades,” ACM Transactions on Graphics, vol. 39, no. 6. Association for Computing Machinery, 2020.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3414685.3417843","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. ACM Transactions on Graphics. 2020;39(6). doi:10.1145/3414685.3417843"},"publication":"ACM Transactions on Graphics","date_published":"2020-11-26T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"26","intvolume":" 39","title":"Computational design of cold bent glass façades","status":"public","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8562","oa_version":"Submitted Version","file":[{"file_name":"coldglass.pdf","access_level":"open_access","file_size":28964641,"content_type":"application/pdf","creator":"bbickel","relation":"main_file","file_id":"13084","date_created":"2023-05-23T20:54:43Z","date_updated":"2023-05-23T20:54:43Z","checksum":"c7f67717ad74e670b7daeae732abe151","success":1}],"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface."}]},{"article_type":"original","page":"5201-5206","publication":"Nano Letters","citation":{"chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01466.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:10.1021/acs.nanolett.0c01466.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01466","ieee":"G. Katsaros et al., “Zero field splitting of heavy-hole states in quantum dots,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206.","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 2020;20(7):5201-5206. doi:10.1021/acs.nanolett.0c01466"},"date_published":"2020-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","status":"public","title":"Zero field splitting of heavy-hole states in quantum dots","ddc":["530"],"intvolume":" 20","_id":"8203","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_NanoLetters_Katsaros.pdf","creator":"dernst","content_type":"application/pdf","file_size":3308906,"file_id":"8204","relation":"main_file","success":1,"date_created":"2020-08-06T09:35:37Z","date_updated":"2020-08-06T09:35:37Z"}],"type":"journal_article","abstract":[{"text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits.","lang":"eng"}],"issue":"7","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"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":["000548893200066"],"pmid":["32479090"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.0c01466","month":"06","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"GeKa"}],"acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","year":"2020","pmid":1,"date_created":"2020-08-06T09:25:04Z","date_updated":"2024-02-21T12:44:01Z","volume":20,"author":[{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip"},{"full_name":"Vukušić, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","first_name":"Lada","last_name":"Vukušić"},{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"full_name":"Gao, Fei","first_name":"Fei","last_name":"Gao"},{"last_name":"Wang","first_name":"Ting","orcid":"0000-0002-4619-9575","full_name":"Wang, Ting"},{"full_name":"Zhang, Jian-Jun","last_name":"Zhang","first_name":"Jian-Jun"},{"last_name":"Held","first_name":"Karsten","full_name":"Held, Karsten"}],"related_material":{"record":[{"id":"7689","status":"public","relation":"research_data"}]},"file_date_updated":"2020-08-06T09:35:37Z","ec_funded":1},{"day":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-10-05T00:00:00Z","publication":"eLife","citation":{"ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 2020;9. doi:10.7554/eLife.61106","ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior,” eLife, vol. 9. eLife Sciences Publications, 2020.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2020). Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.61106","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 9, 61106.","short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, ELife 9 (2020).","mla":"Gridchyn, Igor, et al. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” ELife, vol. 9, 61106, eLife Sciences Publications, 2020, doi:10.7554/eLife.61106.","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.61106."},"article_type":"original","abstract":[{"lang":"eng","text":"In vitro work revealed that excitatory synaptic inputs to hippocampal inhibitory interneurons could undergo Hebbian, associative, or non-associative plasticity. Both behavioral and learning-dependent reorganization of these connections has also been demonstrated by measuring spike transmission probabilities in pyramidal cell-interneuron spike cross-correlations that indicate monosynaptic connections. Here we investigated the activity-dependent modification of these connections during exploratory behavior in rats by optogenetically inhibiting pyramidal cell and interneuron subpopulations. Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_eLife_Gridchyn.pdf","content_type":"application/pdf","file_size":447669,"creator":"dernst","relation":"main_file","file_id":"8749","checksum":"6a7b0543c440f4c000a1864e69377d95","success":1,"date_updated":"2020-11-09T09:17:40Z","date_created":"2020-11-09T09:17:40Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8740","status":"public","ddc":["570"],"title":"Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior","intvolume":" 9","month":"10","publication_identifier":{"eissn":["2050084X"]},"doi":"10.7554/eLife.61106","language":[{"iso":"eng"}],"external_id":{"isi":["000584369000001"]},"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":"FWF","name":"Interneuron plasticity during spatial learning","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"},{"name":"Interneuro Plasticity During Spatial Learning","call_identifier":"FWF","grant_number":"I03713","_id":"2654F984-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-11-09T09:17:40Z","article_number":"61106","author":[{"full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929","first_name":"Igor","last_name":"Gridchyn"},{"last_name":"Schönenberger","first_name":"Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"related_material":{"record":[{"id":"8563","status":"public","relation":"research_data"}]},"date_created":"2020-11-08T23:01:25Z","date_updated":"2024-02-21T12:43:40Z","volume":9,"year":"2020","acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"eLife Sciences Publications"},{"month":"09","day":"21","article_processing_charge":"No","has_accepted_license":"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"},"citation":{"apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8375","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8375.","ama":"Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:10.15479/AT:ISTA:8375","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8375.","short":"R. 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Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8375."},"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"date_published":"2020-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:8375","type":"research_data","abstract":[{"lang":"eng","text":"Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape."}],"file_date_updated":"2020-09-11T09:52:36Z","ec_funded":1,"_id":"8375","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","ddc":["000"],"department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","first_name":"Ruslan","full_name":"Guseinov, Ruslan"}],"contributor":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","contributor_type":"researcher","last_name":"Guseinov"},{"first_name":"Connor","contributor_type":"researcher","last_name":"McMahan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Perez Rodriguez","first_name":"Jesus"},{"last_name":"Daraio","contributor_type":"researcher","first_name":"Chiara"},{"first_name":"Bernd","last_name":"Bickel","contributor_type":"researcher","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"}],"related_material":{"record":[{"id":"8366","status":"public","relation":"used_in_publication"}]},"date_created":"2020-09-11T09:52:54Z","date_updated":"2024-02-21T12:44:29Z","oa_version":"Published Version","file":[{"content_type":"video/mp4","file_size":29214988,"creator":"rguseino","file_name":"supplementary_movie_1.mp4","access_level":"open_access","date_updated":"2020-09-11T09:45:21Z","date_created":"2020-09-11T09:45:21Z","checksum":"4029ffd65fb82ef2366b2fc2a4908e16","success":1,"relation":"main_file","file_id":"8376"},{"file_id":"8377","relation":"main_file","date_created":"2020-09-11T09:45:25Z","date_updated":"2020-09-11T09:45:25Z","success":1,"checksum":"8ed03b04d80f1a4e622cb22e6100afd8","file_name":"supplementary_movie_2.mp4","access_level":"open_access","creator":"rguseino","file_size":28449475,"content_type":"video/mp4"},{"success":1,"checksum":"ad6864afb5e694e5c52a88fba4e02eea","date_updated":"2020-09-11T09:45:28Z","date_created":"2020-09-11T09:45:28Z","file_id":"8378","relation":"main_file","creator":"rguseino","content_type":"video/mp4","file_size":26315853,"access_level":"open_access","file_name":"supplementary_movie_3.mp4"},{"relation":"main_file","file_id":"8379","checksum":"b079cef7871fe1afb69af0e2b099f3b1","success":1,"date_updated":"2020-09-11T09:45:33Z","date_created":"2020-09-11T09:45:33Z","access_level":"open_access","file_name":"supplementary_movie_4.mp4","content_type":"video/mp4","file_size":25198755,"creator":"rguseino"},{"content_type":"video/mp4","file_size":29011354,"creator":"rguseino","file_name":"supplementary_movie_5.mp4","access_level":"open_access","date_created":"2020-09-11T09:45:36Z","date_updated":"2020-09-11T09:45:36Z","checksum":"9d1d48a8ed5c109a999c51b044ee523d","success":1,"relation":"main_file","file_id":"8380"},{"file_id":"8381","relation":"main_file","success":1,"checksum":"d414d0059e982d752d218756b3c3ce05","date_updated":"2020-09-11T09:52:36Z","date_created":"2020-09-11T09:52:36Z","access_level":"open_access","file_name":"readme.txt","creator":"rguseino","content_type":"text/plain","file_size":586}]},{"abstract":[{"text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:02Z","ec_funded":1,"type":"research_data","author":[{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8203"}]},"contributor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","contributor_type":"contact_person","last_name":"Katsaros"}],"date_created":"2020-05-01T15:14:46Z","date_updated":"2024-02-21T12:44:02Z","file":[{"creator":"gkatsaro","file_size":5514403,"content_type":"application/x-zip-compressed","access_level":"open_access","file_name":"DOI_ZeroFieldSplitting.zip","checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","date_updated":"2020-07-14T12:48:02Z","date_created":"2020-05-01T15:13:28Z","file_id":"7786","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7689","year":"2020","status":"public","ddc":["530"],"title":"Supplementary data for \"Zero field splitting of heavy-hole states in quantum dots\"","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","day":"01","month":"05","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-05-01T00:00:00Z","doi":"10.15479/AT:ISTA:7689","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","short":"G. 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Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689"},"project":[{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"},{"name":"Towards scalable hut wire quantum devices","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"}]},{"date_published":"2020-11-23T00:00:00Z","doi":"10.15479/AT:ISTA:8761","acknowledged_ssus":[{"_id":"ScienComp"}],"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":{"ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:10.15479/AT:ISTA:8761","ista":"Guseinov R. 2020. 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Guseinov, (2020).","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8761."},"project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"has_accepted_license":"1","article_processing_charge":"No","month":"11","day":"23","related_material":{"record":[{"id":"8562","status":"public","relation":"used_in_publication"}],"link":[{"relation":"software","url":"https://github.com/russelmann/cold-glass-acm"}]},"contributor":[{"first_name":"Konstantinos","last_name":"Gavriil","contributor_type":"researcher"},{"orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Guseinov","first_name":"Ruslan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Perez Rodriguez","first_name":"Jesus"},{"last_name":"Pellis","contributor_type":"researcher","first_name":"Davide"},{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","contributor_type":"researcher","first_name":"Paul M"},{"first_name":"Florian","contributor_type":"researcher","last_name":"Rist"},{"last_name":"Pottmann","contributor_type":"researcher","first_name":"Helmut"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","contributor_type":"researcher"}],"author":[{"full_name":"Guseinov, Ruslan","first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077"}],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"mdn_model.tar.gz","content_type":"application/x-gzip","file_size":15378270,"creator":"rguseino","relation":"main_file","file_id":"8762","checksum":"f5ae57b97017b9f61081032703361233","success":1,"date_created":"2020-11-16T10:31:29Z","date_updated":"2020-11-16T10:31:29Z"},{"date_created":"2020-11-16T10:43:23Z","date_updated":"2020-11-16T10:43:23Z","success":1,"checksum":"b0d25e04060ee78c585ee2f23542c744","file_id":"8763","relation":"main_file","creator":"rguseino","content_type":"application/x-gzip","file_size":615387734,"file_name":"optimal_panels_data.tar.gz","access_level":"open_access"},{"date_created":"2020-11-18T10:04:59Z","date_updated":"2020-11-18T10:04:59Z","success":1,"checksum":"69c1dde3434ada86d125e0c2588caf1e","file_id":"8770","relation":"main_file","creator":"rguseino","file_size":1228,"content_type":"text/plain","file_name":"readme.txt","access_level":"open_access"}],"date_updated":"2024-02-21T12:43:22Z","date_created":"2020-11-16T10:47:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8761","year":"2020","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","ddc":["000"],"title":"Supplementary data for \"Computational design of cold bent glass façades\"","status":"public","ec_funded":1,"file_date_updated":"2020-11-18T10:04:59Z","type":"research_data"},{"day":"19","month":"10","has_accepted_license":"1","article_processing_charge":"No","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"citation":{"ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563."},"date_published":"2020-10-19T00:00:00Z","doi":"10.15479/AT:ISTA:8563","type":"research_data","file_date_updated":"2020-10-19T10:12:29Z","abstract":[{"lang":"eng","text":"Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife."}],"ddc":["570"],"status":"public","title":"Optogenetic alteration of hippocampal network activity","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8563","year":"2020","date_created":"2020-09-23T14:39:54Z","date_updated":"2024-02-21T12:43:41Z","oa_version":"Published Version","file":[{"checksum":"a16098a6d172f9c42ab5af5f6991668c","success":1,"date_updated":"2020-09-23T14:36:17Z","date_created":"2020-09-23T14:36:17Z","relation":"main_file","file_id":"8564","content_type":"application/x-compressed","file_size":145243906,"creator":"jozsef","access_level":"open_access","file_name":"upload.tgz"},{"relation":"main_file","file_id":"8675","checksum":"0bfc54b7e14c0694cd081617318ba606","success":1,"date_updated":"2020-10-19T10:12:29Z","date_created":"2020-10-19T10:12:29Z","access_level":"open_access","file_name":"redme.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":11648,"creator":"jozsef"}],"author":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"},{"full_name":"Gridchyn, Igor","orcid":"0000-0002-1807-1929","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","last_name":"Gridchyn","first_name":"Igor"},{"first_name":"Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp"}],"contributor":[{"first_name":"Jozsef L","contributor_type":"project_leader","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8740"}]}},{"article_number":"237","file_date_updated":"2020-07-14T12:47:55Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BeBi"}],"year":"2020","date_updated":"2024-02-21T12:45:02Z","date_created":"2020-01-13T16:54:26Z","volume":11,"author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"McMahan, Connor","first_name":"Connor","last_name":"McMahan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus","full_name":"Perez Rodriguez, Jesus"},{"last_name":"Daraio","first_name":"Chiara","full_name":"Daraio, Chiara"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"related_material":{"record":[{"id":"8366","status":"public","relation":"dissertation_contains"},{"relation":"research_data","status":"public","id":"7154"}],"link":[{"url":"https://ist.ac.at/en/news/geometry-meets-time/","relation":"press_release","description":"News on IST Homepage"}]},"month":"01","publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"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":["000511916800015"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-14015-2","type":"journal_article","abstract":[{"lang":"eng","text":"Advances in shape-morphing materials, such as hydrogels, shape-memory polymers and light-responsive polymers have enabled prescribing self-directed deformations of initially flat geometries. However, most proposed solutions evolve towards a target geometry without considering time-dependent actuation paths. To achieve more complex geometries and avoid self-collisions, it is critical to encode a spatial and temporal shape evolution within the initially flat shell. Recent realizations of time-dependent morphing are limited to the actuation of few, discrete hinges and cannot form doubly curved surfaces. Here, we demonstrate a method for encoding temporal shape evolution in architected shells that assume complex shapes and doubly curved geometries. The shells are non-periodic tessellations of pre-stressed contractile unit cells that soften in water at rates prescribed locally by mesostructure geometry. The ensuing midplane contraction is coupled to the formation of encoded curvatures. We propose an inverse design tool based on a data-driven model for unit cells’ temporal responses."}],"title":"Programming temporal morphing of self-actuated shells","status":"public","ddc":["000"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7262","oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Guseinov.pdf","access_level":"open_access","creator":"rguseino","content_type":"application/pdf","file_size":1315270,"file_id":"7336","relation":"main_file","date_created":"2020-01-15T14:35:34Z","date_updated":"2020-07-14T12:47:55Z","checksum":"7db23fef2f4cda712f17f1004116ddff"}],"keyword":["Design","Synthesis and processing","Mechanical engineering","Polymers"],"scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Nature Communications","citation":{"short":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, B. Bickel, Nature Communications 11 (2020).","mla":"Guseinov, Ruslan, et al. “Programming Temporal Morphing of Self-Actuated Shells.” Nature Communications, vol. 11, 237, Springer Nature, 2020, doi:10.1038/s41467-019-14015-2.","chicago":"Guseinov, Ruslan, Connor McMahan, Jesus Perez Rodriguez, Chiara Daraio, and Bernd Bickel. “Programming Temporal Morphing of Self-Actuated Shells.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-019-14015-2.","ama":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. Programming temporal morphing of self-actuated shells. Nature Communications. 2020;11. doi:10.1038/s41467-019-14015-2","apa":"Guseinov, R., McMahan, C., Perez Rodriguez, J., Daraio, C., & Bickel, B. (2020). Programming temporal morphing of self-actuated shells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-14015-2","ieee":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, and B. Bickel, “Programming temporal morphing of self-actuated shells,” Nature Communications, vol. 11. Springer Nature, 2020.","ista":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. 2020. Programming temporal morphing of self-actuated shells. Nature Communications. 11, 237."},"date_published":"2020-01-13T00:00:00Z"},{"month":"12","day":"01","has_accepted_license":"1","article_processing_charge":"No","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","short":"F.K. Schur, (2020).","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592."},"doi":"10.15479/AT:ISTA:14592","date_published":"2020-12-01T00:00:00Z","type":"research_data","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","status":"public","ddc":["570"],"department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14592","year":"2020","date_created":"2023-11-22T15:00:57Z","date_updated":"2024-02-21T12:44:48Z","file":[{"access_level":"open_access","file_name":"3Dprint-files_download_v2.zip","file_size":49297,"content_type":"application/zip","creator":"fschur","relation":"main_file","file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","success":1,"date_created":"2023-11-22T14:58:44Z","date_updated":"2023-11-22T14:58:44Z"},{"relation":"main_file","file_id":"14637","date_created":"2023-12-01T10:39:59Z","date_updated":"2023-12-01T10:39:59Z","checksum":"4c66ddedee4d01c1c4a7978208350cfc","success":1,"file_name":"readme.txt","access_level":"open_access","content_type":"text/plain","file_size":641,"creator":"cchlebak"}],"oa_version":"Published Version","author":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"related_material":{"record":[{"id":"8586","relation":"research_data","status":"public"}]},"contributor":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","contributor_type":"researcher"},{"first_name":"Bettina","contributor_type":"researcher","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","contributor_type":"researcher","last_name":"Hauschild"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","contributor_type":"researcher"}]},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","publication":"Complex Networks and their applications VIII","citation":{"ista":"Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.","apa":"Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In Complex Networks and their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-36687-2_3","ieee":"S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in Complex Networks and their applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.","ama":"Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: Complex Networks and Their Applications VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3","chicago":"Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In Complex Networks and Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3.","mla":"Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3.","short":"S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39."},"page":"27-39","abstract":[{"lang":"eng","text":"Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis."}],"type":"conference","alternative_title":["SCI"],"oa_version":"Submitted Version","file":[{"success":1,"checksum":"8951f094c8c7dae9ff8db885199bc296","date_updated":"2020-10-08T08:16:48Z","date_created":"2020-10-08T08:16:48Z","file_id":"8625","relation":"main_file","creator":"bchatter","file_size":310598,"content_type":"application/pdf","access_level":"open_access","file_name":"main.pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"7213","title":"A persistent homology perspective to the link prediction problem","status":"public","ddc":["004"],"intvolume":" 881","month":"01","publication_identifier":{"issn":["1860949X"],"isbn":["9783030366865"],"eissn":["18609503"]},"conference":{"name":"COMPLEX: International Conference on Complex Networks and their Applications","end_date":"2019-12-12","start_date":"2019-12-10","location":"Lisbon, Portugal"},"doi":"10.1007/978-3-030-36687-2_3","language":[{"iso":"eng"}],"external_id":{"isi":["000843927300003"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"file_date_updated":"2020-10-08T08:16:48Z","ec_funded":1,"author":[{"last_name":"Bhatia","first_name":"Sumit","full_name":"Bhatia, Sumit"},{"full_name":"Chatterjee, Bapi","last_name":"Chatterjee","first_name":"Bapi","orcid":"0000-0002-2742-4028","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nathani, Deepak","last_name":"Nathani","first_name":"Deepak"},{"first_name":"Manohar","last_name":"Kaul","full_name":"Kaul, Manohar"}],"date_updated":"2024-02-22T13:16:06Z","date_created":"2019-12-29T23:00:45Z","volume":881,"year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaAl"}]},{"date_created":"2021-12-16T13:23:27Z","date_updated":"2024-02-22T13:10:45Z","author":[{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Malkhi, Dahlia","first_name":"Dahlia","last_name":"Malkhi"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"}],"publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols.","year":"2020","language":[{"iso":"eng"}],"conference":{"location":"Virtual, United States","start_date":"2020-11-09","end_date":"2020-11-13","name":"CCS: Computer and Communications Security"},"doi":"10.1145/3372297.3423364","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2019/1015","open_access":"1"}],"oa":1,"external_id":{"isi":["000768470400104"]},"month":"10","publication_identifier":{"isbn":["978-1-4503-7089-9"]},"oa_version":"Preprint","status":"public","title":"Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10556","abstract":[{"lang":"eng","text":"In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Virtual, United States, 2020, pp. 1751–1767.","apa":"Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. https://doi.org/10.1145/3372297.3423364","ama":"Kokoris Kogias E, Malkhi D, Spiegelman A. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In: Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364","chicago":"Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, 1751–1767. Association for Computing Machinery, 2020. https://doi.org/10.1145/3372297.3423364.","mla":"Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364.","short":"E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767."},"day":"30","article_processing_charge":"No","scopus_import":"1"},{"oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"main.pdf","file_size":1125794,"content_type":"application/pdf","creator":"mgarcias","relation":"main_file","file_id":"9203","checksum":"8f97f229316c3b3a6f0cf99297aa0941","date_updated":"2021-02-26T16:38:14Z","date_created":"2021-02-26T16:38:14Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"9202","status":"public","ddc":["000"],"title":"Hybridization for stability verification of nonlinear switched systems","abstract":[{"lang":"eng","text":"We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function."}],"type":"conference","date_published":"2020-12-01T00:00:00Z","publication":"2020 IEEE Real-Time Systems Symposium","citation":{"chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” In 2020 IEEE Real-Time Systems Symposium, 244–56. IEEE, 2020. https://doi.org/10.1109/RTSS49844.2020.00031.","mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–56, doi:10.1109/RTSS49844.2020.00031.","short":"M. Garcia Soto, P. Prabhakar, in:, 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–256.","ista":"Garcia Soto M, Prabhakar P. 2020. Hybridization for stability verification of nonlinear switched systems. 2020 IEEE Real-Time Systems Symposium. RTTS: Real-Time Systems Symposium, 244–256.","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Hybridization for stability verification of nonlinear switched systems. In 2020 IEEE Real-Time Systems Symposium (pp. 244–256). Houston, TX, USA : IEEE. https://doi.org/10.1109/RTSS49844.2020.00031","ieee":"M. Garcia Soto and P. Prabhakar, “Hybridization for stability verification of nonlinear switched systems,” in 2020 IEEE Real-Time Systems Symposium, Houston, TX, USA , 2020, pp. 244–256.","ama":"Garcia Soto M, Prabhakar P. Hybridization for stability verification of nonlinear switched systems. In: 2020 IEEE Real-Time Systems Symposium. IEEE; 2020:244-256. doi:10.1109/RTSS49844.2020.00031"},"page":"244-256","day":"01","has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Garcia Soto","first_name":"Miriam","orcid":"0000-0003-2936-5719","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Soto, Miriam"},{"first_name":"Pavithra","last_name":"Prabhakar","full_name":"Prabhakar, Pavithra"}],"date_updated":"2024-02-22T13:25:19Z","date_created":"2021-02-26T16:38:24Z","acknowledgement":"Miriam Garc´ıa Soto was partially supported by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Pavithra Prabhakar was partially supported by NSF CAREER Award No. 1552668, NSF Award No. 2008957 and ONR YIP Award No. N000141712577.","year":"2020","publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"file_date_updated":"2021-02-26T16:38:14Z","conference":{"name":"RTTS: Real-Time Systems Symposium","end_date":"2020-12-04","location":"Houston, TX, USA ","start_date":"2020-12-01"},"doi":"10.1109/RTSS49844.2020.00031","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000680435100021"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"month":"12","publication_identifier":{"eisbn":["9781728183244"],"eissn":["2576-3172"]}},{"ec_funded":1,"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","year":"2020","date_created":"2019-09-24T17:30:59Z","date_updated":"2024-02-22T13:33:02Z","volume":376,"author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","first_name":"Chiara","full_name":"Boccato, Chiara"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"full_name":"Cenatiempo, Serena","first_name":"Serena","last_name":"Cenatiempo"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"month":"06","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000536053300012"],"arxiv":["1812.03086"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.03086"}],"language":[{"iso":"eng"}],"doi":"10.1007/s00220-019-03555-9","type":"journal_article","abstract":[{"lang":"eng","text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential."}],"status":"public","title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","intvolume":" 376","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6906","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"1311-1395","publication":"Communications in Mathematical Physics","citation":{"short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395.","mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics, vol. 376, Springer, 2020, pp. 1311–95, doi:10.1007/s00220-019-03555-9.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics. Springer, 2020. https://doi.org/10.1007/s00220-019-03555-9.","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 2020;376:1311-1395. doi:10.1007/s00220-019-03555-9","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-019-03555-9","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” Communications in Mathematical Physics, vol. 376. Springer, pp. 1311–1395, 2020.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395."},"date_published":"2020-06-01T00:00:00Z"},{"date_published":"2020-01-01T00:00:00Z","page":"319-341","publication":"Gastrulation: From Embryonic Pattern to Form","citation":{"ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. Gastrulation: From Embryonic Pattern to Form. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:10.1016/bs.ctdb.2019.07.001","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","apa":"Bruce, A. E. E., & Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 319–341). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.07.001","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:10.1016/bs.ctdb.2019.07.001.","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.07.001."},"day":"01","article_processing_charge":"No","series_title":"Current Topics in Developmental Biology","scopus_import":"1","oa_version":"None","title":"Mechanisms of zebrafish epiboly: A current view","status":"public","intvolume":" 136","_id":"7410","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed."}],"type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1016/bs.ctdb.2019.07.001","quality_controlled":"1","isi":1,"external_id":{"isi":["000611830600012"]},"month":"01","publication_identifier":{"isbn":["9780128127988"],"issn":["0070-2153"]},"date_created":"2020-01-30T09:24:06Z","date_updated":"2024-02-22T13:23:09Z","volume":136,"author":[{"full_name":"Bruce, Ashley E.E.","last_name":"Bruce","first_name":"Ashley E.E."},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"publication_status":"published","editor":[{"last_name":"Solnica-Krezel","first_name":"Lilianna ","full_name":"Solnica-Krezel, Lilianna "}],"publisher":"Elsevier","department":[{"_id":"CaHe"}],"year":"2020"},{"file":[{"file_name":"2019_IJCV_Sun.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1715072,"creator":"dernst","relation":"main_file","file_id":"7110","date_created":"2019-11-26T10:30:02Z","date_updated":"2020-07-14T12:47:45Z","checksum":"155e63edf664dcacb3bdc1c2223e606f"}],"oa_version":"Published Version","ddc":["004"],"title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","status":"public","intvolume":" 128","_id":"6944","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2020-04-01T00:00:00Z","article_type":"original","page":"970-995","publication":"International Journal of Computer Vision","citation":{"apa":"Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” International Journal of Computer Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 2020;128(4):970-995. doi:10.1007/s11263-019-01232-x","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x.","short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.","mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x."},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_updated":"2024-02-22T14:57:30Z","date_created":"2019-10-14T09:14:28Z","volume":128,"author":[{"full_name":"Sun, Rémy","last_name":"Sun","first_name":"Rémy"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6482"}],"link":[{"url":"https://doi.org/10.1007/s11263-019-01262-5","relation":"erratum"}]},"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Springer Nature","year":"2020","file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/s11263-019-01232-x","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"external_id":{"isi":["000494406800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"04","publication_identifier":{"issn":["0920-5691"],"eissn":["1573-1405"]}},{"publication_identifier":{"eissn":["2475-1421"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1145/3371093","project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1902.04744"]},"oa":1,"file_date_updated":"2020-09-01T11:12:58Z","article_number":"25","volume":4,"date_created":"2020-08-30T22:01:12Z","date_updated":"2024-02-22T15:16:45Z","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.3533633","relation":"software"}]},"author":[{"full_name":"Wang, Peixin","last_name":"Wang","first_name":"Peixin"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Deng, Yuxin","last_name":"Deng","first_name":"Yuxin"},{"first_name":"Ming","last_name":"Xu","full_name":"Xu, Ming"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2020","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","citation":{"ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093."},"publication":"Proceedings of the ACM on Programming Languages","issue":"POPL","abstract":[{"text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature.","lang":"eng"}],"type":"conference","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8328","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"date_created":"2020-09-01T11:12:58Z","date_updated":"2020-09-01T11:12:58Z","access_level":"open_access","file_name":"2019_ACM_POPL_Wang.pdf","file_size":564151,"content_type":"application/pdf","creator":"cziletti"}],"intvolume":" 4","status":"public","ddc":["004"],"title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8324"},{"date_published":"2020-01-01T00:00:00Z","page":"27-36","article_type":"original","citation":{"ama":"Salazar JE, Severin D, Vega Zuniga TA, et al. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 2020;94(1-4):27-36. doi:10.1159/000504162","ista":"Salazar JE, Severin D, Vega Zuniga TA, Fernández-Aburto P, Deichler A, Sallaberry A. M, Mpodozis J. 2020. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 94(1–4), 27–36.","ieee":"J. E. Salazar et al., “Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes),” Brain, Behavior and Evolution, vol. 94, no. 1–4. Karger Publishers, pp. 27–36, 2020.","apa":"Salazar, J. E., Severin, D., Vega Zuniga, T. A., Fernández-Aburto, P., Deichler, A., Sallaberry A., M., & Mpodozis, J. (2020). Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. Karger Publishers. https://doi.org/10.1159/000504162","mla":"Salazar, Juan Esteban, et al. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution, vol. 94, no. 1–4, Karger Publishers, 2020, pp. 27–36, doi:10.1159/000504162.","short":"J.E. Salazar, D. Severin, T.A. Vega Zuniga, P. Fernández-Aburto, A. Deichler, M. Sallaberry A., J. Mpodozis, Brain, Behavior and Evolution 94 (2020) 27–36.","chicago":"Salazar, Juan Esteban, Daniel Severin, Tomas A Vega Zuniga, Pedro Fernández-Aburto, Alfonso Deichler, Michel Sallaberry A., and Jorge Mpodozis. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution. Karger Publishers, 2020. https://doi.org/10.1159/000504162."},"publication":"Brain, Behavior and Evolution","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","intvolume":" 94","status":"public","title":"Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"7160","issue":"1-4","abstract":[{"text":"Nocturnal animals that rely on their visual system for foraging, mating, and navigation usually exhibit specific traits associated with living in scotopic conditions. Most nocturnal birds have several visual specializations, such as enlarged eyes and an increased orbital convergence. However, the actual role of binocular vision in nocturnal foraging is still debated. Nightjars (Aves: Caprimulgidae) are predators that actively pursue and capture flying insects in crepuscular and nocturnal environments, mainly using a conspicuous “sit-and-wait” tactic on which pursuit begins with an insect flying over the bird that sits on the ground. In this study, we describe the visual system of the band-winged nightjar (Systellura longirostris), with emphasis on anatomical features previously described as relevant for nocturnal birds. Orbit convergence, determined by 3D scanning of the skull, was 73.28°. The visual field, determined by ophthalmoscopic reflex, exhibits an area of maximum binocular overlap of 42°, and it is dorsally oriented. The eyes showed a nocturnal-like normalized corneal aperture/axial length index. Retinal ganglion cells (RGCs) were relatively scant, and distributed in an unusual oblique-band pattern, with higher concentrations in the ventrotemporal quadrant. Together, these results indicate that the band-winged nightjar exhibits a retinal specialization associated with the binocular area of their dorsal visual field, a relevant area for pursuit triggering and prey attacks. The RGC distribution observed is unusual among birds, but similar to that of some visually dependent insectivorous bats, suggesting that those features might be convergent in relation to feeding strategies.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1159/000504162","quality_controlled":"1","isi":1,"external_id":{"isi":["000522856600004"],"pmid":["31751995"]},"publication_identifier":{"eissn":["1421-9743"],"issn":["0006-8977"]},"month":"01","volume":94,"date_updated":"2024-02-22T15:18:34Z","date_created":"2019-12-09T09:04:13Z","author":[{"full_name":"Salazar, Juan Esteban","first_name":"Juan Esteban","last_name":"Salazar"},{"first_name":"Daniel","last_name":"Severin","full_name":"Severin, Daniel"},{"full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","last_name":"Vega Zuniga"},{"last_name":"Fernández-Aburto","first_name":"Pedro","full_name":"Fernández-Aburto, Pedro"},{"full_name":"Deichler, Alfonso","first_name":"Alfonso","last_name":"Deichler"},{"last_name":"Sallaberry A.","first_name":"Michel","full_name":"Sallaberry A., Michel"},{"first_name":"Jorge","last_name":"Mpodozis","full_name":"Mpodozis, Jorge"}],"department":[{"_id":"MaJö"}],"publisher":"Karger Publishers","publication_status":"published","pmid":1,"year":"2020"},{"related_material":{"record":[{"id":"149","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"6179"}]},"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"volume":48,"date_updated":"2024-02-22T14:34:33Z","date_created":"2019-03-28T09:20:08Z","year":"2020","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","ec_funded":1,"doi":"10.1214/19-AOP1379","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1804.07744"],"isi":["000528269100013"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.07744","open_access":"1"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0091-1798"]},"month":"03","oa_version":"Preprint","_id":"6184","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 48","title":"Correlated random matrices: Band rigidity and edge universality","status":"public","issue":"2","abstract":[{"lang":"eng","text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models."}],"type":"journal_article","date_published":"2020-03-01T00:00:00Z","citation":{"ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020.","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379.","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001."},"publication":"Annals of Probability","page":"963-1001","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["32087370"]},"quality_controlled":"1","doi":"10.1016/j.molp.2020.02.012","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["1674-2052"]},"year":"2020","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"EvBe"}],"author":[{"last_name":"Moulinier-Anzola","first_name":"Jeanette","full_name":"Moulinier-Anzola, Jeanette"},{"full_name":"Schwihla, Maximilian","first_name":"Maximilian","last_name":"Schwihla"},{"first_name":"Lucinda","last_name":"De-Araújo","full_name":"De-Araújo, Lucinda"},{"first_name":"Christina","last_name":"Artner","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","full_name":"Artner, Christina"},{"last_name":"Jörg","first_name":"Lisa","full_name":"Jörg, Lisa"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"},{"first_name":"Barbara","last_name":"Korbei","full_name":"Korbei, Barbara"}],"date_updated":"2024-02-28T12:41:52Z","date_created":"2024-02-28T08:55:56Z","volume":13,"file_date_updated":"2024-02-28T12:39:56Z","publication":"Molecular Plant","citation":{"ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012."},"article_type":"original","page":"717-731","date_published":"2020-05-04T00:00:00Z","keyword":["Plant Science","Molecular Biology"],"day":"04","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15037","status":"public","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","ddc":["580"],"intvolume":" 13","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3089212,"access_level":"open_access","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","success":1,"checksum":"c538a5008f7827f62d17d40a3bfabe65","date_updated":"2024-02-28T12:39:56Z","date_created":"2024-02-28T12:39:56Z","file_id":"15038","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.","lang":"eng"}],"issue":"5"},{"title":"Molecular recognition at septin interfaces: The switches hold the key","status":"public","intvolume":" 432","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15036","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"issue":"21","article_type":"original","page":"5784-5801","publication":"Journal of Molecular Biology","citation":{"ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001."},"date_published":"2020-10-02T00:00:00Z","keyword":["Molecular Biology","Structural Biology"],"day":"02","article_processing_charge":"No","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Elsevier","year":"2020","pmid":1,"date_updated":"2024-02-28T12:37:54Z","date_created":"2024-02-28T08:50:34Z","volume":432,"author":[{"full_name":"Rosa, Higor Vinícius Dias","first_name":"Higor Vinícius Dias","last_name":"Rosa"},{"first_name":"Diego Antonio","last_name":"Leonardo","full_name":"Leonardo, Diego Antonio"},{"full_name":"Brognara, Gabriel","last_name":"Brognara","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"first_name":"José","last_name":"Brandão-Neto","full_name":"Brandão-Neto, José"},{"first_name":"Humberto","last_name":"D'Muniz Pereira","full_name":"D'Muniz Pereira, Humberto"},{"full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo","first_name":"Ana Paula Ulian"},{"full_name":"Garratt, Richard Charles","first_name":"Richard Charles","last_name":"Garratt"}],"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.jmb.2020.09.001","open_access":"1"}],"external_id":{"pmid":["32910969"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2020.09.001","month":"10","publication_identifier":{"issn":["0022-2836"]}},{"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1145/3386569.3392405","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000583700300004"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392405"}],"oa":1,"month":"07","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"date_updated":"2024-02-28T12:57:31Z","date_created":"2020-09-13T22:01:18Z","volume":39,"author":[{"full_name":"Ishida, Sadashige","last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"},{"first_name":"Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter"},{"last_name":"Narita","first_name":"Fumiya","full_name":"Narita, Fumiya"},{"full_name":"Hachisuka, Toshiya","last_name":"Hachisuka","first_name":"Toshiya"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","year":"2020","file_date_updated":"2020-11-23T09:03:19Z","ec_funded":1,"article_number":"31","date_published":"2020-07-08T00:00:00Z","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31."},"day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":14935529,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_soapfilm_submitted.pdf","success":1,"checksum":"813831ca91319d794d9748c276b24578","date_created":"2020-11-23T09:03:19Z","date_updated":"2020-11-23T09:03:19Z","file_id":"8795","relation":"main_file"}],"ddc":["000"],"status":"public","title":"A model for soap film dynamics with evolving thickness","intvolume":" 39","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8384","abstract":[{"lang":"eng","text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film."}],"issue":"4","type":"journal_article"},{"type":"conference","issue":"7","abstract":[{"lang":"eng","text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17]."}],"status":"public","title":"Graph sparsification for derandomizing massively parallel computation with low space","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7802","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"175-185","citation":{"chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282"},"publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","date_published":"2020-07-01T00:00:00Z","ec_funded":1,"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2020","date_updated":"2024-02-28T12:53:09Z","date_created":"2020-05-06T08:53:34Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"9541"}]},"author":[{"full_name":"Czumaj, Artur","first_name":"Artur","last_name":"Czumaj","orcid":"0000-0002-5646-9524"},{"full_name":"Davies, Peter","last_name":"Davies","first_name":"Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"last_name":"Parter","first_name":"Merav","full_name":"Parter, Merav"}],"month":"07","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1912.05390"],"isi":["000744436200015"]},"main_file_link":[{"url":"https://arxiv.org/abs/1912.05390","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3350755.3400282","conference":{"end_date":"2020-07-17","location":"Virtual Event, United States","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"}},{"date_published":"2020-02-19T00:00:00Z","page":"276-291","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542","apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542."},"day":"19","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Non-blocking interpolation search trees with doubly-logarithmic running time","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7636","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22","location":"San Diego, CA, United States","end_date":"2020-02-26"},"doi":"10.1145/3332466.3374542","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"oa":1,"external_id":{"isi":["000564476500020"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"month":"02","publication_identifier":{"isbn":["9781450368186"]},"date_updated":"2024-02-28T12:55:14Z","date_created":"2020-04-05T22:00:49Z","author":[{"first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"first_name":"Aleksandar","last_name":"Prokopec","full_name":"Prokopec, Aleksandar"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","year":"2020","ec_funded":1}]