[{"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"14","status":"public","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"citation":{"apa":"Schmid, L., Hilbe, C., Chatterjee, K., &#38; Nowak, M. (2022). Direct reciprocity between individuals that use different strategy spaces. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">https://doi.org/10.1371/journal.pcbi.1010149</a>","chicago":"Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">https://doi.org/10.1371/journal.pcbi.1010149</a>.","mla":"Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” <i>PLOS Computational Biology</i>, vol. 18, no. 6, e1010149, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">10.1371/journal.pcbi.1010149</a>.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","ieee":"L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between individuals that use different strategy spaces,” <i>PLOS Computational Biology</i>, vol. 18, no. 6. Public Library of Science, 2022.","ista":"Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 18(6), e1010149.","ama":"Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals that use different strategy spaces. <i>PLOS Computational Biology</i>. 2022;18(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010149\">10.1371/journal.pcbi.1010149</a>"},"acknowledgement":"This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG 863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","type":"journal_article","article_type":"original","intvolume":"        18","oa_version":"Published Version","_id":"12280","scopus_import":"1","oa":1,"file_date_updated":"2023-01-30T11:28:13Z","isi":1,"publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"date_updated":"2025-04-14T07:52:47Z","month":"06","language":[{"iso":"eng"}],"date_published":"2022-06-14T00:00:00Z","article_number":"e1010149","year":"2022","date_created":"2023-01-16T10:02:51Z","publication":"PLOS Computational Biology","issue":"6","doi":"10.1371/journal.pcbi.1010149","publication_identifier":{"eissn":["1553-7358"]},"quality_controlled":"1","file":[{"file_id":"12460","date_updated":"2023-01-30T11:28:13Z","file_size":3143222,"checksum":"31b6b311b6731f1658277a9dfff6632c","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_PlosCompBio_Schmid.pdf","date_created":"2023-01-30T11:28:13Z","creator":"dernst","success":1}],"corr_author":"1","ddc":["000","570"],"has_accepted_license":"1","volume":18,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Laura","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329"},{"last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"pmid":1,"abstract":[{"text":"In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate.","lang":"eng"}],"external_id":{"isi":["000843626800031"],"pmid":["35700167"]},"publication_status":"published","article_processing_charge":"No","title":"Direct reciprocity between individuals that use different strategy spaces","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"]},{"volume":28,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Chiara","last_name":"Franceschini","full_name":"Franceschini, Chiara"},{"full_name":"Gonçalves, Patrícia","last_name":"Gonçalves","first_name":"Patrícia"},{"last_name":"Sau","first_name":"Federico","full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"publication_status":"published","external_id":{"arxiv":["2007.11998"],"isi":["000766619100025"]},"abstract":[{"text":"We study the hydrodynamic and hydrostatic limits of the one-dimensional open symmetric inclusion process with slow boundary. Depending on the value of the parameter tuning the interaction rate of the bulk of the system with the boundary, we obtain a linear heat equation with either Dirichlet, Robin or Neumann boundary conditions as hydrodynamic equation. In our approach, we combine duality and first-second class particle techniques to reduce the scaling limit of the inclusion process to the limiting behavior of a single, non-interacting, particle.","lang":"eng"}],"article_processing_charge":"No","page":"1340-1381","keyword":["Statistics and Probability"],"title":"Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics","date_created":"2023-01-16T10:03:04Z","year":"2022","publication":"Bernoulli","publication_identifier":{"issn":["1350-7265"]},"doi":"10.3150/21-bej1390","issue":"2","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.11998"}],"type":"journal_article","acknowledgement":"C.F. and P.G. thank FCT/Portugal for support through the project UID/MAT/04459/2013.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovative programme (grant agreement No. 715734). F.S. was founded by the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.\r\nF.S. wishes to thank Joe P. Chen for some fruitful discussions at an early stage of this work. F.S. thanks CAMGSD, IST, Lisbon, where part of this work has been done, and the European research and innovative programme No. 715734 for the kind hospitality.","oa_version":"Preprint","intvolume":"        28","article_type":"original","scopus_import":"1","_id":"12281","oa":1,"isi":1,"date_updated":"2025-04-14T07:44:00Z","arxiv":1,"department":[{"_id":"JaMa"}],"publisher":"Bernoulli Society for Mathematical Statistics and Probability","date_published":"2022-05-01T00:00:00Z","language":[{"iso":"eng"}],"month":"05","ec_funded":1,"status":"public","day":"01","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"ieee":"C. Franceschini, P. Gonçalves, and F. Sau, “Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics,” <i>Bernoulli</i>, vol. 28, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1340–1381, 2022.","short":"C. Franceschini, P. Gonçalves, F. Sau, Bernoulli 28 (2022) 1340–1381.","ista":"Franceschini C, Gonçalves P, Sau F. 2022. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. Bernoulli. 28(2), 1340–1381.","ama":"Franceschini C, Gonçalves P, Sau F. Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. <i>Bernoulli</i>. 2022;28(2):1340-1381. doi:<a href=\"https://doi.org/10.3150/21-bej1390\">10.3150/21-bej1390</a>","apa":"Franceschini, C., Gonçalves, P., &#38; Sau, F. (2022). Symmetric inclusion process with slow boundary: Hydrodynamics and hydrostatics. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/21-bej1390\">https://doi.org/10.3150/21-bej1390</a>","chicago":"Franceschini, Chiara, Patrícia Gonçalves, and Federico Sau. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2022. <a href=\"https://doi.org/10.3150/21-bej1390\">https://doi.org/10.3150/21-bej1390</a>.","mla":"Franceschini, Chiara, et al. “Symmetric Inclusion Process with Slow Boundary: Hydrodynamics and Hydrostatics.” <i>Bernoulli</i>, vol. 28, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2022, pp. 1340–81, doi:<a href=\"https://doi.org/10.3150/21-bej1390\">10.3150/21-bej1390</a>."}},{"scopus_import":"1","_id":"12282","acknowledgement":"The authors want to thank Professors Carrie Bernecky, Tom Henzinger, Martin Loose and Gaia Novarino for accepting to be interviewed, thus giving significant contribution to the discussion that lead to this article.","type":"journal_article","intvolume":"       135","oa_version":"None","article_type":"letter_note","date_updated":"2024-10-09T21:03:55Z","publisher":"The Company of Biologists","department":[{"_id":"SiHi"},{"_id":"LeSa"}],"date_published":"2022-04-19T00:00:00Z","month":"04","language":[{"iso":"eng"}],"isi":1,"status":"public","day":"19","citation":{"mla":"Amberg, Nicole, et al. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” <i>Journal of Cell Science</i>, vol. 135, no. 8, 260017, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.260017\">10.1242/jcs.260017</a>.","apa":"Amberg, N., Stouffer, M. A., &#38; Vercellino, I. (2022). Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.260017\">https://doi.org/10.1242/jcs.260017</a>","chicago":"Amberg, Nicole, Melissa A Stouffer, and Irene Vercellino. “Operation STEM Fatale – How an Equity, Diversity and Inclusion Initiative Has Brought Us to Reflect on the Current Challenges in Cell Biology and Science as a Whole.” <i>Journal of Cell Science</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.260017\">https://doi.org/10.1242/jcs.260017</a>.","ista":"Amberg N, Stouffer MA, Vercellino I. 2022. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. Journal of Cell Science. 135(8), 260017.","ama":"Amberg N, Stouffer MA, Vercellino I. Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole. <i>Journal of Cell Science</i>. 2022;135(8). doi:<a href=\"https://doi.org/10.1242/jcs.260017\">10.1242/jcs.260017</a>","ieee":"N. Amberg, M. A. Stouffer, and I. Vercellino, “Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole,” <i>Journal of Cell Science</i>, vol. 135, no. 8. The Company of Biologists, 2022.","short":"N. Amberg, M.A. Stouffer, I. Vercellino, Journal of Cell Science 135 (2022)."},"pmid":1,"volume":135,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stouffer","first_name":"Melissa A","id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","full_name":"Stouffer, Melissa A"},{"first_name":"Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene"}],"title":"Operation STEM fatale – how an equity, diversity and inclusion initiative has brought us to reflect on the current challenges in cell biology and science as a whole","external_id":{"isi":["000798123600015"],"pmid":["35438168"]},"publication_status":"published","abstract":[{"lang":"eng","text":"From a simple thought to a multicellular movement"}],"article_processing_charge":"No","publication":"Journal of Cell Science","doi":"10.1242/jcs.260017","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"issue":"8","article_number":"260017","date_created":"2023-01-16T10:03:14Z","year":"2022","quality_controlled":"1","corr_author":"1"},{"author":[{"first_name":"Joseph","last_name":"Atherton","full_name":"Atherton, Joseph"},{"id":"4C9372C4-F248-11E8-B48F-1D18A9856A87","full_name":"Stouffer, Melissa A","last_name":"Stouffer","first_name":"Melissa A"},{"first_name":"Fiona","last_name":"Francis","full_name":"Francis, Fiona"},{"first_name":"Carolyn A.","last_name":"Moores","full_name":"Moores, Carolyn A."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":135,"pmid":1,"article_processing_charge":"No","publication_status":"published","external_id":{"pmid":["35383828"],"isi":["000783840400010"]},"abstract":[{"lang":"eng","text":"Neurons extend axons to form the complex circuitry of the mature brain. This depends on the coordinated response and continuous remodelling of the microtubule and F-actin networks in the axonal growth cone. Growth cone architecture remains poorly understood at nanoscales. We therefore investigated mouse hippocampal neuron growth cones using cryo-electron tomography to directly visualise their three-dimensional subcellular architecture with molecular detail. Our data showed that the hexagonal arrays of actin bundles that form filopodia penetrate and terminate deep within the growth cone interior. We directly observed the modulation of these and other growth cone actin bundles by alteration of individual F-actin helical structures. Microtubules with blunt, slightly flared or gently curved ends predominated in the growth cone, frequently contained lumenal particles and exhibited lattice defects. Investigation of the effect of absence of doublecortin, a neurodevelopmental cytoskeleton regulator, on growth cone cytoskeleton showed no major anomalies in overall growth cone organisation or in F-actin subpopulations. However, our data suggested that microtubules sustained more structural defects, highlighting the importance of microtubule integrity during growth cone migration."}],"keyword":["Cell Biology"],"title":"Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography","date_created":"2023-01-16T10:03:24Z","year":"2022","article_number":"259234","doi":"10.1242/jcs.259234","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"issue":"7","publication":"Journal of Cell Science","quality_controlled":"1","file":[{"access_level":"open_access","relation":"main_file","checksum":"4346ed32cb7c89a8ca051c7da68a9a1c","file_size":13868733,"date_updated":"2023-01-30T11:41:01Z","file_id":"12461","success":1,"creator":"dernst","date_created":"2023-01-30T11:41:01Z","file_name":"2022_JourCellBiology_Atherton.pdf","content_type":"application/pdf"}],"has_accepted_license":"1","ddc":["570"],"oa_version":"Published Version","intvolume":"       135","article_type":"original","acknowledgement":"J.A. was supported by a grant from the Medical Research Council (MRC), UK (MR/R000352/1) to C.A.M. Cryo-EM data were collected on equipment funded by the Wellcome Trust, UK (079605/Z/06/Z) and the Biotechnology and Biological Sciences Research Council (BBSRC) UK (BB/L014211/1). F.F.’s salary and institute were supported by Inserm (Institut National de la Santé et de la Recherche Médicale), CNRS (Centre National de la Recherche Scientifique) and Sorbonne Université. F.F.’s group was particularly supported by Agence Nationale de la\r\nRecherche (ANR-16-CE16-0011-03) and Seventh Framework Programme (EUHEALTH-\r\n2013, DESIRE, N° 60253; also funding M.S.’s salary) and the European Cooperation in Science and Technology (COST Action CA16118). Open Access funding provided by Birkbeck College: Birkbeck University of London. Deposited in PMC for immediate release.","type":"journal_article","scopus_import":"1","_id":"12283","isi":1,"file_date_updated":"2023-01-30T11:41:01Z","oa":1,"date_published":"2022-04-01T00:00:00Z","month":"04","language":[{"iso":"eng"}],"date_updated":"2023-08-04T10:28:34Z","publisher":"The Company of Biologists","department":[{"_id":"SiHi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"01","citation":{"mla":"Atherton, Joseph, et al. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” <i>Journal of Cell Science</i>, vol. 135, no. 7, 259234, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.259234\">10.1242/jcs.259234</a>.","chicago":"Atherton, Joseph, Melissa A Stouffer, Fiona Francis, and Carolyn A. Moores. “Visualising the Cytoskeletal Machinery in Neuronal Growth Cones Using Cryo-Electron Tomography.” <i>Journal of Cell Science</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.259234\">https://doi.org/10.1242/jcs.259234</a>.","apa":"Atherton, J., Stouffer, M. A., Francis, F., &#38; Moores, C. A. (2022). Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.259234\">https://doi.org/10.1242/jcs.259234</a>","ama":"Atherton J, Stouffer MA, Francis F, Moores CA. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. <i>Journal of Cell Science</i>. 2022;135(7). doi:<a href=\"https://doi.org/10.1242/jcs.259234\">10.1242/jcs.259234</a>","ista":"Atherton J, Stouffer MA, Francis F, Moores CA. 2022. Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Journal of Cell Science. 135(7), 259234.","short":"J. Atherton, M.A. Stouffer, F. Francis, C.A. Moores, Journal of Cell Science 135 (2022).","ieee":"J. Atherton, M. A. Stouffer, F. Francis, and C. A. Moores, “Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography,” <i>Journal of Cell Science</i>, vol. 135, no. 7. The Company of Biologists, 2022."}},{"article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000892204300001"],"pmid":["36040301"]},"abstract":[{"lang":"eng","text":"To understand the function of neuronal circuits, it is crucial to disentangle the connectivity patterns within the network. However, most tools currently used to explore connectivity have low throughput, low selectivity, or limited accessibility. Here, we report the development of an improved packaging system for the production of the highly neurotropic RVdGenvA-CVS-N2c rabies viral vectors, yielding titers orders of magnitude higher with no background contamination, at a fraction of the production time, while preserving the efficiency of transsynaptic labeling. Along with the production pipeline, we developed suites of ‘starter’ AAV and bicistronic RVdG-CVS-N2c vectors, enabling retrograde labeling from a wide range of neuronal populations, tailored for diverse experimental requirements. We demonstrate the power and flexibility of the new system by uncovering hidden local and distal inhibitory connections in the mouse hippocampal formation and by imaging the functional properties of a cortical microcircuit across weeks. Our novel production pipeline provides a convenient approach to generate new rabies vectors, while our toolkit flexibly and efficiently expands the current capacity to label, manipulate and image the neuronal activity of interconnected neuronal circuits in vitro and in vivo."}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"title":"Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Anton L","last_name":"Sumser","full_name":"Sumser, Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881"},{"first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav"}],"volume":11,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"corr_author":"1","quality_controlled":"1","file":[{"file_id":"12463","relation":"main_file","checksum":"5a2a65e3e7225090c3d8199f3bbd7b7b","access_level":"open_access","date_updated":"2023-01-30T11:50:53Z","file_size":8506811,"date_created":"2023-01-30T11:50:53Z","file_name":"2022_eLife_Sumser.pdf","content_type":"application/pdf","creator":"dernst","success":1}],"has_accepted_license":"1","ddc":["570"],"date_created":"2023-01-16T10:04:15Z","year":"2022","article_number":"79848","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/elife.79848","publication":"eLife","isi":1,"file_date_updated":"2023-01-30T11:50:53Z","oa":1,"date_published":"2022-09-15T00:00:00Z","language":[{"iso":"eng"}],"month":"09","date_updated":"2025-04-15T08:29:05Z","department":[{"_id":"MaJö"},{"_id":"PeJo"}],"publisher":"eLife Sciences Publications","intvolume":"        11","oa_version":"Published Version","article_type":"original","acknowledgement":"We thank F Marr for technical assistance, A Murray for RVdG-CVS-N2c viruses and Neuro2A packaging cell-lines and J Watson for reading the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Imaging and Optics Facility (IOF) and the Preclinical Facility (PCF). This project was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC advanced grant No 692692, PJ, ERC starting grant No 756502, MJ), the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, PJ), the Human Frontier Science Program (LT000256/2018-L, AS) and EMBO (ALTF 1098-2017, AS).","type":"journal_article","scopus_import":"1","_id":"12288","citation":{"mla":"Sumser, Anton L., et al. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>, vol. 11, 79848, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>.","chicago":"Sumser, Anton L, Maximilian A Jösch, Peter M Jonas, and Yoav Ben Simon. “Fast, High-Throughput Production of Improved Rabies Viral Vectors for Specific, Efficient and Versatile Transsynaptic Retrograde Labeling.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>.","apa":"Sumser, A. L., Jösch, M. A., Jonas, P. M., &#38; Ben Simon, Y. (2022). Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.79848\">https://doi.org/10.7554/elife.79848</a>","ista":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. 2022. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. eLife. 11, 79848.","ama":"Sumser AL, Jösch MA, Jonas PM, Ben Simon Y. Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.79848\">10.7554/elife.79848</a>","short":"A.L. Sumser, M.A. Jösch, P.M. Jonas, Y. Ben Simon, ELife 11 (2022).","ieee":"A. L. Sumser, M. A. Jösch, P. M. Jonas, and Y. Ben Simon, “Fast, high-throughput production of improved rabies viral vectors for specific, efficient and versatile transsynaptic retrograde labeling,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"15","status":"public"},{"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"12","status":"public","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"citation":{"short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 27 (2022) 1–38.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal multi-resolvent local laws for Wigner matrices,” <i>Electronic Journal of Probability</i>, vol. 27. Institute of Mathematical Statistics, pp. 1–38, 2022.","ama":"Cipolloni G, Erdös L, Schröder DJ. Optimal multi-resolvent local laws for Wigner matrices. <i>Electronic Journal of Probability</i>. 2022;27:1-38. doi:<a href=\"https://doi.org/10.1214/22-ejp838\">10.1214/22-ejp838</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Optimal multi-resolvent local laws for Wigner matrices. Electronic Journal of Probability. 27, 1–38.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Multi-Resolvent Local Laws for Wigner Matrices.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/22-ejp838\">https://doi.org/10.1214/22-ejp838</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Optimal multi-resolvent local laws for Wigner matrices. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-ejp838\">https://doi.org/10.1214/22-ejp838</a>","mla":"Cipolloni, Giorgio, et al. “Optimal Multi-Resolvent Local Laws for Wigner Matrices.” <i>Electronic Journal of Probability</i>, vol. 27, Institute of Mathematical Statistics, 2022, pp. 1–38, doi:<a href=\"https://doi.org/10.1214/22-ejp838\">10.1214/22-ejp838</a>."},"acknowledgement":"L. Erdős was supported by ERC Advanced Grant “RMTBeyond” No. 101020331. D. Schröder was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","type":"journal_article","article_type":"original","intvolume":"        27","oa_version":"Published Version","_id":"12290","scopus_import":"1","oa":1,"file_date_updated":"2023-01-30T11:59:21Z","isi":1,"department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","date_updated":"2025-04-14T07:57:19Z","language":[{"iso":"eng"}],"month":"09","date_published":"2022-09-12T00:00:00Z","year":"2022","date_created":"2023-01-16T10:04:38Z","publication":"Electronic Journal of Probability","doi":"10.1214/22-ejp838","publication_identifier":{"eissn":["1083-6489"]},"file":[{"file_id":"12464","date_updated":"2023-01-30T11:59:21Z","file_size":502149,"access_level":"open_access","relation":"main_file","checksum":"bb647b48fbdb59361210e425c220cdcb","file_name":"2022_ElecJournProbability_Cipolloni.pdf","content_type":"application/pdf","date_created":"2023-01-30T11:59:21Z","success":1,"creator":"dernst"}],"quality_controlled":"1","corr_author":"1","ddc":["510"],"has_accepted_license":"1","volume":27,"author":[{"full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","first_name":"Giorgio"},{"last_name":"Erdös","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"We prove local laws, i.e. optimal concentration estimates for arbitrary products of resolvents of a Wigner random matrix with deterministic matrices in between. We find that the size of such products heavily depends on whether some of the deterministic matrices are traceless. Our estimates correctly account for this dependence and they hold optimally down to the smallest possible spectral scale.","lang":"eng"}],"external_id":{"isi":["000910863700003"]},"publication_status":"published","page":"1-38","article_processing_charge":"No","title":"Optimal multi-resolvent local laws for Wigner matrices","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"]},{"citation":{"apa":"Kumar, R., Reichelt, M., &#38; Bisht, N. C. (2022). An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis. In J. Jez (Ed.), <i>Biochemical Pathways and Environmental Responses in Plants: Part A</i> (Vol. 676, pp. 49–69). Elsevier. <a href=\"https://doi.org/10.1016/bs.mie.2022.07.019\">https://doi.org/10.1016/bs.mie.2022.07.019</a>","chicago":"Kumar, Roshan, Michael Reichelt, and Naveen C. Bisht. “An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis.” In <i>Biochemical Pathways and Environmental Responses in Plants: Part A</i>, edited by Joseph Jez, 676:49–69. Elsevier, 2022. <a href=\"https://doi.org/10.1016/bs.mie.2022.07.019\">https://doi.org/10.1016/bs.mie.2022.07.019</a>.","mla":"Kumar, Roshan, et al. “An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis.” <i>Biochemical Pathways and Environmental Responses in Plants: Part A</i>, edited by Joseph Jez, vol. 676, Elsevier, 2022, pp. 49–69, doi:<a href=\"https://doi.org/10.1016/bs.mie.2022.07.019\">10.1016/bs.mie.2022.07.019</a>.","ieee":"R. Kumar, M. Reichelt, and N. C. Bisht, “An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis,” in <i>Biochemical Pathways and Environmental Responses in Plants: Part A</i>, vol. 676, J. Jez, Ed. Elsevier, 2022, pp. 49–69.","short":"R. Kumar, M. Reichelt, N.C. Bisht, in:, J. Jez (Ed.), Biochemical Pathways and Environmental Responses in Plants: Part A, Elsevier, 2022, pp. 49–69.","ista":"Kumar R, Reichelt M, Bisht NC. 2022.An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis. In: Biochemical Pathways and Environmental Responses in Plants: Part A. Methods in Enzymology, vol. 676, 49–69.","ama":"Kumar R, Reichelt M, Bisht NC. An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis. In: Jez J, ed. <i>Biochemical Pathways and Environmental Responses in Plants: Part A</i>. Vol 676. Elsevier; 2022:49-69. doi:<a href=\"https://doi.org/10.1016/bs.mie.2022.07.019\">10.1016/bs.mie.2022.07.019</a>"},"alternative_title":["Methods in Enzymology"],"status":"public","day":"21","language":[{"iso":"eng"}],"month":"10","date_published":"2022-10-21T00:00:00Z","publisher":"Elsevier","date_updated":"2025-07-03T14:02:58Z","_id":"12294","scopus_import":"1","intvolume":"       676","oa_version":"None","type":"book_chapter","quality_controlled":"1","publication_identifier":{"isbn":["9780323955614"],"issn":["0076-6879"]},"doi":"10.1016/bs.mie.2022.07.019","publication":"Biochemical Pathways and Environmental Responses in Plants: Part A","year":"2022","date_created":"2023-01-16T10:05:13Z","title":"An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis","page":"49-69","article_processing_charge":"No","abstract":[{"text":"Brassicaceae are blessed with specialized metabolites called glucosinolates (GSLs), which along with their degradation products, are beneficial in agriculture and human health. To date, more than 130 GSL structures have been identified, mostly derived from the amino acid methionine. The biosynthesis of methionine-derived aliphatic GSLs starts with a side-chain elongation step involving a recursive three-step cyclic process that incorporates a new methylene group into the 2-oxo acid to form a series of elongated 2-oxo acids. Methylthioalkylmalate synthase (MAMS) catalyzes the first committed step in the side-chain elongation of methionine-derived GSLs. The substrate specificity of MAMS with different 2-oxo acids determines whether reaction products of a given cycle enter for an additional round of chain elongation or enter into core GSLs structure formation. Multiple MAMS encoding genes are present in the Brassicaceae species and are known to play a central role in shaping the diverse profile of aliphatic GSLs. We recently established a highly sensitive LC-MS/MS-based methodology that quantifies the MAMS activity by estimating the amount of the next intermediate of the pathway, the 2-malate derivatives. Overall, this chapter describes the protocol for the expression, purification, and steady-state kinetic analysis of the recombinant MAMS protein.","lang":"eng"}],"external_id":{"pmid":["36280361"]},"publication_status":"published","pmid":1,"author":[{"last_name":"Kumar","first_name":"Roshan","full_name":"Kumar, Roshan","id":"50e95140-3016-11ec-9e1a-881b648a1367","orcid":"0000-0002-0346-9125"},{"full_name":"Reichelt, Michael","last_name":"Reichelt","first_name":"Michael"},{"full_name":"Bisht, Naveen C.","last_name":"Bisht","first_name":"Naveen C."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"last_name":"Jez","first_name":"Joseph","full_name":"Jez, Joseph"}],"volume":676},{"oa":1,"isi":1,"date_updated":"2025-09-10T09:52:23Z","arxiv":1,"publisher":"Springer Nature","department":[{"_id":"ElKo"}],"date_published":"2022-10-22T00:00:00Z","month":"10","language":[{"iso":"eng"}],"type":"conference","acknowledgement":"We thank our shepherd Aniket Kate and the anonymous reviewers at FC 2022 for their helpful feedback. This work is supported by the Novi team at Facebook. We also thank the Novi Research and Engineering teams for valuable feedback, and in particular Mathieu Baudet, Andrey Chursin, George Danezis, Zekun Li, and Dahlia Malkhi for discussions that shaped this work.","oa_version":"Preprint","intvolume":"     13411","scopus_import":"1","_id":"12298","citation":{"chicago":"Gelashvili, Rati, Eleftherios Kokoris Kogias, Alberto Sonnino, Alexander Spiegelman, and Zhuolun Xiang. “Jolteon and Ditto: Network-Adaptive Efficient Consensus with Asynchronous Fallback.” In <i>Financial Cryptography and Data Security</i>, 13411:296–315. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">https://doi.org/10.1007/978-3-031-18283-9_14</a>.","apa":"Gelashvili, R., Kokoris Kogias, E., Sonnino, A., Spiegelman, A., &#38; Xiang, Z. (2022). Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. In <i>Financial Cryptography and Data Security</i> (Vol. 13411, pp. 296–315). Radisson Grenada Beach Resort, Grenada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">https://doi.org/10.1007/978-3-031-18283-9_14</a>","mla":"Gelashvili, Rati, et al. “Jolteon and Ditto: Network-Adaptive Efficient Consensus with Asynchronous Fallback.” <i>Financial Cryptography and Data Security</i>, vol. 13411, Springer Nature, 2022, pp. 296–315, doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">10.1007/978-3-031-18283-9_14</a>.","ieee":"R. Gelashvili, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, and Z. Xiang, “Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback,” in <i>Financial Cryptography and Data Security</i>, Radisson Grenada Beach Resort, Grenada, 2022, vol. 13411, pp. 296–315.","short":"R. Gelashvili, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, Z. Xiang, in:, Financial Cryptography and Data Security, Springer Nature, 2022, pp. 296–315.","ama":"Gelashvili R, Kokoris Kogias E, Sonnino A, Spiegelman A, Xiang Z. Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. In: <i>Financial Cryptography and Data Security</i>. Vol 13411. Springer Nature; 2022:296-315. doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_14\">10.1007/978-3-031-18283-9_14</a>","ista":"Gelashvili R, Kokoris Kogias E, Sonnino A, Spiegelman A, Xiang Z. 2022. Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback. Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 13411, 296–315."},"status":"public","day":"22","alternative_title":["LNCS"],"external_id":{"isi":["001423640200014"],"arxiv":["2106.10362"]},"publication_status":"published","abstract":[{"text":"Existing committee-based Byzantine state machine replication (SMR) protocols, typically deployed in production blockchains, face a clear trade-off: (1) they either achieve linear communication cost in the steady state, but sacrifice liveness during periods of asynchrony, or (2) they are robust (progress with probability one) but pay quadratic communication cost. We believe this trade-off is unwarranted since existing linear protocols still have asymptotic quadratic cost in the worst case. We design Ditto, a Byzantine SMR protocol that enjoys the best of both worlds: optimal communication on and off the steady state (linear and quadratic, respectively) and progress guarantee under asynchrony and DDoS attacks. We achieve this by replacing the view-synchronization of partially synchronous protocols with an asynchronous fallback mechanism at no extra asymptotic cost. Specifically, we start from HotStuff, a state-of-the-art linear protocol, and gradually build Ditto. As a separate contribution and an intermediate step, we design a 2-chain version of HotStuff, Jolteon, which leverages a quadratic view-change mechanism to reduce the latency of the standard 3-chain HotStuff. We implement and experimentally evaluate all our systems to prove that breaking the robustness-efficiency trade-off is in the realm of practicality.","lang":"eng"}],"article_processing_charge":"No","page":"296-315","title":"Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback","volume":13411,"author":[{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Sonnino, Alberto","first_name":"Alberto","last_name":"Sonnino"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"},{"full_name":"Xiang, Zhuolun","first_name":"Zhuolun","last_name":"Xiang"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","conference":{"location":"Radisson Grenada Beach Resort, Grenada","end_date":"2022-05-06","start_date":"2022-05-02","name":"FC: Financial Cryptography"},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2106.10362"}],"date_created":"2023-01-16T10:05:51Z","year":"2022","publication":"Financial Cryptography and Data Security","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031182839"],"issn":["0302-9743"],"isbn":["9783031182822"]},"doi":"10.1007/978-3-031-18283-9_14"},{"alternative_title":["LNCS"],"status":"public","day":"06","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"chicago":"Doveri, Kyveli, Pierre Ganty, and Nicolas Adrien Mazzocchi. “FORQ-Based Language Inclusion Formal Testing.” In <i>Computer Aided Verification</i>, 13372:109–29. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">https://doi.org/10.1007/978-3-031-13188-2_6</a>.","apa":"Doveri, K., Ganty, P., &#38; Mazzocchi, N. A. (2022). FORQ-based language inclusion formal testing. In <i>Computer Aided Verification</i> (Vol. 13372, pp. 109–129). Haifa, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">https://doi.org/10.1007/978-3-031-13188-2_6</a>","mla":"Doveri, Kyveli, et al. “FORQ-Based Language Inclusion Formal Testing.” <i>Computer Aided Verification</i>, vol. 13372, Springer Nature, 2022, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">10.1007/978-3-031-13188-2_6</a>.","ieee":"K. Doveri, P. Ganty, and N. A. Mazzocchi, “FORQ-based language inclusion formal testing,” in <i>Computer Aided Verification</i>, Haifa, Israel, 2022, vol. 13372, pp. 109–129.","short":"K. Doveri, P. Ganty, N.A. Mazzocchi, in:, Computer Aided Verification, Springer Nature, 2022, pp. 109–129.","ista":"Doveri K, Ganty P, Mazzocchi NA. 2022. FORQ-based language inclusion formal testing. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13372, 109–129.","ama":"Doveri K, Ganty P, Mazzocchi NA. FORQ-based language inclusion formal testing. In: <i>Computer Aided Verification</i>. Vol 13372. Springer Nature; 2022:109-129. doi:<a href=\"https://doi.org/10.1007/978-3-031-13188-2_6\">10.1007/978-3-031-13188-2_6</a>"},"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"_id":"12302","scopus_import":"1","oa_version":"Published Version","intvolume":"     13372","acknowledgement":"This work was partially funded by the ESF Investing in your future, the Madrid regional project S2018/TCS-4339 BLOQUES, the Spanish project PGC2018-102210-B-I00 BOSCO, the Ramón y Cajal fellowship RYC-2016-20281, and the ERC grant PR1001ERC02.","type":"conference","language":[{"iso":"eng"}],"month":"08","date_published":"2022-08-06T00:00:00Z","publisher":"Springer Nature","arxiv":1,"department":[{"_id":"ToHe"}],"date_updated":"2025-04-14T07:55:56Z","isi":1,"oa":1,"file_date_updated":"2023-01-30T12:51:02Z","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031131875"],"issn":["0302-9743"],"eisbn":["9783031131882"]},"doi":"10.1007/978-3-031-13188-2_6","publication":"Computer Aided Verification","year":"2022","date_created":"2023-01-16T10:06:31Z","has_accepted_license":"1","conference":{"end_date":"2022-08-10","location":"Haifa, Israel","name":"CAV: Computer Aided Verification","start_date":"2022-08-07"},"ddc":["000"],"quality_controlled":"1","file":[{"file_name":"2022_LNCS_Doveri.pdf","content_type":"application/pdf","date_created":"2023-01-30T12:51:02Z","success":1,"creator":"dernst","file_id":"12465","date_updated":"2023-01-30T12:51:02Z","file_size":497682,"access_level":"open_access","relation":"main_file","checksum":"edc363b1be5447a09063e115c247918a"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Doveri","first_name":"Kyveli","full_name":"Doveri, Kyveli"},{"last_name":"Ganty","first_name":"Pierre","full_name":"Ganty, Pierre"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien"}],"volume":13372,"title":"FORQ-based language inclusion formal testing","page":"109-129","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We propose a novel algorithm to decide the language inclusion between (nondeterministic) Büchi automata, a PSPACE-complete problem. Our approach, like others before, leverage a notion of quasiorder to prune the search for a counterexample by discarding candidates which are subsumed by others for the quasiorder. Discarded candidates are guaranteed to not compromise the completeness of the algorithm. The novelty of our work lies in the quasiorder used to discard candidates. We introduce FORQs (family of right quasiorders) that we obtain by adapting the notion of family of right congruences put forward by Maler and Staiger in 1993. We define a FORQ-based inclusion algorithm which we prove correct and instantiate it for a specific FORQ, called the structural FORQ, induced by the Büchi automaton to the right of the inclusion sign. The resulting implementation, called FORKLIFT, scales up better than the state-of-the-art on a variety of benchmarks including benchmarks from program verification and theorem proving for word combinatorics. Artifact: https://doi.org/10.5281/zenodo.6552870"}],"publication_status":"published","external_id":{"arxiv":["2207.13549"],"isi":["000870310500006"]}},{"title":"Loop Grassmannians of Quivers and Affine Quantum Groups","abstract":[{"lang":"eng","text":"We construct for each choice of a quiver Q, a cohomology theory A, and a poset P a “loop Grassmannian” GP(Q,A). This generalizes loop Grassmannians of semisimple groups and the loop Grassmannians of based quadratic forms. The addition of a “dilation” torus D⊆G2m gives a quantization GPD(Q,A). This construction is motivated by the program of introducing an inner cohomology theory in algebraic geometry adequate for the Geometric Langlands program (Mirković, Some extensions of the notion of loop Grassmannians. Rad Hrvat. Akad. Znan. Umjet. Mat. Znan., the Mardešić issue. No. 532, 53–74, 2017) and on the construction of affine quantum groups from generalized cohomology theories (Yang and Zhao, Quiver varieties and elliptic quantum groups, preprint. arxiv1708.01418)."}],"external_id":{"arxiv":["1810.10095"]},"publication_status":"published","page":"347-392","article_processing_charge":"No","editor":[{"first_name":"Vladimir","last_name":"Baranovskky","full_name":"Baranovskky, Vladimir"},{"full_name":"Guay, Nicolas","last_name":"Guay","first_name":"Nicolas"},{"full_name":"Schedler, Travis","last_name":"Schedler","first_name":"Travis"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Mirković, Ivan","first_name":"Ivan","last_name":"Mirković"},{"full_name":"Yang, Yaping","first_name":"Yaping","last_name":"Yang"},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","full_name":"Zhao, Gufang","first_name":"Gufang","last_name":"Zhao"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1810.10095","open_access":"1"}],"quality_controlled":"1","publication":"Representation Theory and Algebraic Geometry","publication_identifier":{"isbn":["9783030820060"],"issn":["2297-0215"],"eisbn":["9783030820077"],"eissn":["2297-024X"]},"doi":"10.1007/978-3-030-82007-7_8","year":"2022","date_created":"2023-01-16T10:06:41Z","publisher":"Springer Nature; Birkhäuser","arxiv":1,"department":[{"_id":"TaHa"}],"date_updated":"2025-04-14T09:12:46Z","language":[{"iso":"eng"}],"month":"06","date_published":"2022-06-16T00:00:00Z","oa":1,"edition":"1","_id":"12303","scopus_import":"1","acknowledgement":"I.M. thanks Zhijie Dong for long-term discussions on the material that entered this work. We thank Misha Finkelberg for pointing out errors in earlier versions. His advice and his insistence have led to a much better paper. A part of the writing was done at the conference at IST (Vienna) attended by all coauthors. We therefore thank the organizers of the conference and the support of ERC Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593. The work of I.M. was partially supported by NSF grants. The work of Y.Y. was partially supported by the Australian Research Council (ARC) via the award DE190101231. The work of G.Z. was partially supported by ARC via the award DE190101222.","type":"book_chapter","oa_version":"Preprint","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces"}],"citation":{"ama":"Mirković I, Yang Y, Zhao G. Loop Grassmannians of Quivers and Affine Quantum Groups. In: Baranovskky V, Guay N, Schedler T, eds. <i>Representation Theory and Algebraic Geometry</i>. 1st ed. TM. Cham: Springer Nature; Birkhäuser; 2022:347-392. doi:<a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">10.1007/978-3-030-82007-7_8</a>","ista":"Mirković I, Yang Y, Zhao G. 2022.Loop Grassmannians of Quivers and Affine Quantum Groups. In: Representation Theory and Algebraic Geometry. Trends in Mathematics, , 347–392.","ieee":"I. Mirković, Y. Yang, and G. Zhao, “Loop Grassmannians of Quivers and Affine Quantum Groups,” in <i>Representation Theory and Algebraic Geometry</i>, 1st ed., V. Baranovskky, N. Guay, and T. Schedler, Eds. Cham: Springer Nature; Birkhäuser, 2022, pp. 347–392.","short":"I. Mirković, Y. Yang, G. Zhao, in:, V. Baranovskky, N. Guay, T. Schedler (Eds.), Representation Theory and Algebraic Geometry, 1st ed., Springer Nature; Birkhäuser, Cham, 2022, pp. 347–392.","mla":"Mirković, Ivan, et al. “Loop Grassmannians of Quivers and Affine Quantum Groups.” <i>Representation Theory and Algebraic Geometry</i>, edited by Vladimir Baranovskky et al., 1st ed., Springer Nature; Birkhäuser, 2022, pp. 347–92, doi:<a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">10.1007/978-3-030-82007-7_8</a>.","chicago":"Mirković, Ivan, Yaping Yang, and Gufang Zhao. “Loop Grassmannians of Quivers and Affine Quantum Groups.” In <i>Representation Theory and Algebraic Geometry</i>, edited by Vladimir Baranovskky, Nicolas Guay, and Travis Schedler, 1st ed., 347–92. TM. Cham: Springer Nature; Birkhäuser, 2022. <a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">https://doi.org/10.1007/978-3-030-82007-7_8</a>.","apa":"Mirković, I., Yang, Y., &#38; Zhao, G. (2022). Loop Grassmannians of Quivers and Affine Quantum Groups. In V. Baranovskky, N. Guay, &#38; T. Schedler (Eds.), <i>Representation Theory and Algebraic Geometry</i> (1st ed., pp. 347–392). Cham: Springer Nature; Birkhäuser. <a href=\"https://doi.org/10.1007/978-3-030-82007-7_8\">https://doi.org/10.1007/978-3-030-82007-7_8</a>"},"status":"public","day":"16","series_title":"TM","alternative_title":["Trends in Mathematics"],"place":"Cham","ec_funded":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"De Nitti","first_name":"Nicola","full_name":"De Nitti, Nicola"},{"full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer"}],"volume":47,"keyword":["Applied Mathematics","Analysis"],"title":"Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation","article_processing_charge":"No","page":"1394-1434","publication_status":"published","external_id":{"arxiv":["1907.05342"],"isi":["000805689800001"]},"abstract":[{"text":"We establish sharp criteria for the instantaneous propagation of free boundaries in solutions to the thin-film equation. The criteria are formulated in terms of the initial distribution of mass (as opposed to previous almost-optimal results), reflecting the fact that mass is a locally conserved quantity for the thin-film equation. In the regime of weak slippage, our criteria are at the same time necessary and sufficient. The proof of our upper bounds on free boundary propagation is based on a strategy of “propagation of degeneracy” down to arbitrarily small spatial scales: We combine estimates on the local mass and estimates on energies to show that “degeneracy” on a certain space-time cylinder entails “degeneracy” on a spatially smaller space-time cylinder with the same time horizon. The derivation of our lower bounds on free boundary propagation is based on a combination of a monotone quantity and almost optimal estimates established previously by the second author with a new estimate connecting motion of mass to entropy production.","lang":"eng"}],"publication_identifier":{"eissn":["1532-4133"],"issn":["0360-5302"]},"doi":"10.1080/03605302.2022.2056702","issue":"7","publication":"Communications in Partial Differential Equations","date_created":"2023-01-16T10:06:50Z","year":"2022","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1907.05342"}],"corr_author":"1","quality_controlled":"1","scopus_import":"1","_id":"12304","intvolume":"        47","oa_version":"Preprint","article_type":"original","type":"journal_article","acknowledgement":"N. De Nitti acknowledges the kind hospitality of IST Austria within the framework of the ISTernship Summer Program 2018, during which most of the present article was written. N. DeNitti has received funding by The Austrian Agency for International Cooperation in Education &Research (OeAD-GmbH) via its financial support of the ISTernship Summer Program 2018. N.De Nitti would also like to thank Giuseppe Coclite, Giuseppe Devillanova, Giuseppe Florio, Sebastian Hensel, and Francesco Maddalena for several helpful conversations on topics related to this work.","date_published":"2022-07-01T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2024-10-09T21:03:57Z","department":[{"_id":"JuFi"}],"arxiv":1,"publisher":"Taylor & Francis","isi":1,"oa":1,"status":"public","day":"01","citation":{"ista":"De Nitti N, Fischer JL. 2022. Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. Communications in Partial Differential Equations. 47(7), 1394–1434.","ama":"De Nitti N, Fischer JL. Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. <i>Communications in Partial Differential Equations</i>. 2022;47(7):1394-1434. doi:<a href=\"https://doi.org/10.1080/03605302.2022.2056702\">10.1080/03605302.2022.2056702</a>","short":"N. De Nitti, J.L. Fischer, Communications in Partial Differential Equations 47 (2022) 1394–1434.","ieee":"N. De Nitti and J. L. Fischer, “Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation,” <i>Communications in Partial Differential Equations</i>, vol. 47, no. 7. Taylor &#38; Francis, pp. 1394–1434, 2022.","mla":"De Nitti, Nicola, and Julian L. Fischer. “Sharp Criteria for the Waiting Time Phenomenon in Solutions to the Thin-Film Equation.” <i>Communications in Partial Differential Equations</i>, vol. 47, no. 7, Taylor &#38; Francis, 2022, pp. 1394–434, doi:<a href=\"https://doi.org/10.1080/03605302.2022.2056702\">10.1080/03605302.2022.2056702</a>.","chicago":"De Nitti, Nicola, and Julian L Fischer. “Sharp Criteria for the Waiting Time Phenomenon in Solutions to the Thin-Film Equation.” <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/03605302.2022.2056702\">https://doi.org/10.1080/03605302.2022.2056702</a>.","apa":"De Nitti, N., &#38; Fischer, J. L. (2022). Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation. <i>Communications in Partial Differential Equations</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/03605302.2022.2056702\">https://doi.org/10.1080/03605302.2022.2056702</a>"}},{"type":"journal_article","article_type":"original","oa_version":"Preprint","intvolume":"        54","_id":"12305","scopus_import":"1","oa":1,"isi":1,"publisher":"Society for Industrial and Applied Mathematics","arxiv":1,"department":[{"_id":"JuFi"}],"date_updated":"2024-10-09T21:03:58Z","language":[{"iso":"eng"}],"month":"01","date_published":"2022-01-04T00:00:00Z","status":"public","day":"04","citation":{"mla":"Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact Angle Close to 90°.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 114–72, doi:<a href=\"https://doi.org/10.1137/21m1424925\">10.1137/21m1424925</a>.","chicago":"Abels, Helmut, and Maximilian Moser. “Convergence of the Allen--Cahn Equation with a Nonlinear Robin Boundary Condition to Mean Curvature Flow with Contact Angle Close to 90°.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21m1424925\">https://doi.org/10.1137/21m1424925</a>.","apa":"Abels, H., &#38; Moser, M. (2022). Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21m1424925\">https://doi.org/10.1137/21m1424925</a>","ama":"Abels H, Moser M. Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):114-172. doi:<a href=\"https://doi.org/10.1137/21m1424925\">10.1137/21m1424925</a>","ista":"Abels H, Moser M. 2022. Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°. SIAM Journal on Mathematical Analysis. 54(1), 114–172.","short":"H. Abels, M. Moser, SIAM Journal on Mathematical Analysis 54 (2022) 114–172.","ieee":"H. Abels and M. Moser, “Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 114–172, 2022."},"volume":54,"author":[{"first_name":"Helmut","last_name":"Abels","full_name":"Abels, Helmut"},{"id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","full_name":"Moser, Maximilian","first_name":"Maximilian","last_name":"Moser"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"This paper is concerned with the sharp interface limit for the Allen--Cahn equation with a nonlinear Robin boundary condition in a bounded smooth domain Ω⊂\\R2. We assume that a diffuse interface already has developed and that it is in contact with the boundary ∂Ω. The boundary condition is designed in such a way that the limit problem is given by the mean curvature flow with constant α-contact angle. For α close to 90° we prove a local in time convergence result for well-prepared initial data for times when a smooth solution to the limit problem exists. Based on the latter we construct a suitable curvilinear coordinate system and carry out a rigorous asymptotic expansion for the Allen--Cahn equation with the nonlinear Robin boundary condition. Moreover, we show a spectral estimate for the corresponding linearized Allen--Cahn operator and with its aid we derive strong norm estimates for the difference of the exact and approximate solutions using a Gronwall-type argument.","lang":"eng"}],"external_id":{"arxiv":["2105.08434"],"isi":["000762768000004"]},"publication_status":"published","page":"114-172","article_processing_charge":"No","title":"Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"year":"2022","date_created":"2023-01-16T10:07:00Z","publication":"SIAM Journal on Mathematical Analysis","issue":"1","doi":"10.1137/21m1424925","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"quality_controlled":"1","corr_author":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.08434","open_access":"1"}]},{"volume":32,"author":[{"full_name":"Shipman, Barbara A.","first_name":"Barbara A.","last_name":"Shipman"},{"first_name":"Elizabeth R","last_name":"Stephenson","orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Education","General Mathematics"],"title":"Tangible topology through the lens of limits","publication_status":"published","abstract":[{"text":"Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.","lang":"eng"}],"article_processing_charge":"No","page":"593-609","publication":"PRIMUS","doi":"10.1080/10511970.2021.1872750","publication_identifier":{"eissn":["1935-4053"],"issn":["1051-1970"]},"issue":"5","date_created":"2023-01-16T10:07:21Z","year":"2022","quality_controlled":"1","corr_author":"1","scopus_import":"1","_id":"12307","type":"journal_article","intvolume":"        32","oa_version":"None","article_type":"original","date_updated":"2024-10-09T21:03:58Z","publisher":"Taylor & Francis","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"date_published":"2022-05-28T00:00:00Z","language":[{"iso":"eng"}],"month":"05","status":"public","day":"28","citation":{"mla":"Shipman, Barbara A., and Elizabeth R. Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>, vol. 32, no. 5, Taylor &#38; Francis, 2022, pp. 593–609, doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>.","apa":"Shipman, B. A., &#38; Stephenson, E. R. (2022). Tangible topology through the lens of limits. <i>PRIMUS</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>","chicago":"Shipman, Barbara A., and Elizabeth R Stephenson. “Tangible Topology through the Lens of Limits.” <i>PRIMUS</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/10511970.2021.1872750\">https://doi.org/10.1080/10511970.2021.1872750</a>.","ama":"Shipman BA, Stephenson ER. Tangible topology through the lens of limits. <i>PRIMUS</i>. 2022;32(5):593-609. doi:<a href=\"https://doi.org/10.1080/10511970.2021.1872750\">10.1080/10511970.2021.1872750</a>","ista":"Shipman BA, Stephenson ER. 2022. Tangible topology through the lens of limits. PRIMUS. 32(5), 593–609.","ieee":"B. A. Shipman and E. R. Stephenson, “Tangible topology through the lens of limits,” <i>PRIMUS</i>, vol. 32, no. 5. Taylor &#38; Francis, pp. 593–609, 2022.","short":"B.A. Shipman, E.R. Stephenson, PRIMUS 32 (2022) 593–609."}},{"volume":20,"author":[{"last_name":"Mlynarski","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["36542662"],"isi":["000925192000001"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments."}],"article_processing_charge":"No","page":"e3001889","title":"Efficient coding theory of dynamic attentional modulation","date_created":"2023-01-22T23:00:55Z","year":"2022","publication":"PLoS Biology","doi":"10.1371/journal.pbio.3001889","publication_identifier":{"eissn":["1545-7885"]},"issue":"12","quality_controlled":"1","file":[{"file_id":"12337","file_size":4248838,"date_updated":"2023-01-23T08:46:40Z","access_level":"open_access","relation":"main_file","checksum":"5d7f1111a87e5f2c1bf92f8886738894","file_name":"2022_PloSBiology_Mlynarski.pdf","content_type":"application/pdf","date_created":"2023-01-23T08:46:40Z","success":1,"creator":"dernst"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","acknowledgement":"We thank Robbe Goris for generously providing figures from his work and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","type":"journal_article","intvolume":"        20","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"12332","file_date_updated":"2023-01-23T08:46:40Z","oa":1,"isi":1,"date_updated":"2025-06-11T13:57:01Z","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","date_published":"2022-12-21T00:00:00Z","month":"12","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"status":"public","day":"21","project":[{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.","ieee":"W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” <i>PLoS Biology</i>, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.","ama":"Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. 2022;20(12):e3001889. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>","ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","chicago":"Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>.","apa":"Mlynarski, W. F., &#38; Tkačik, G. (2022). Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>","mla":"Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>."}},{"citation":{"mla":"Tomanek, Isabella, and Calin C. Guet. “Adaptation Dynamics between Copynumber and Point Mutations.” <i>ELife</i>, vol. 11, e82240, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/ELIFE.82240\">10.7554/ELIFE.82240</a>.","apa":"Tomanek, I., &#38; Guet, C. C. (2022). Adaptation dynamics between copynumber and point mutations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/ELIFE.82240\">https://doi.org/10.7554/ELIFE.82240</a>","chicago":"Tomanek, Isabella, and Calin C Guet. “Adaptation Dynamics between Copynumber and Point Mutations.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/ELIFE.82240\">https://doi.org/10.7554/ELIFE.82240</a>.","ista":"Tomanek I, Guet CC. 2022. Adaptation dynamics between copynumber and point mutations. eLife. 11, e82240.","ama":"Tomanek I, Guet CC. Adaptation dynamics between copynumber and point mutations. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/ELIFE.82240\">10.7554/ELIFE.82240</a>","short":"I. Tomanek, C.C. Guet, ELife 11 (2022).","ieee":"I. Tomanek and C. C. Guet, “Adaptation dynamics between copynumber and point mutations,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"22","file_date_updated":"2023-01-23T08:56:21Z","oa":1,"isi":1,"date_updated":"2025-03-06T14:03:50Z","department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","date_published":"2022-12-22T00:00:00Z","month":"12","language":[{"iso":"eng"}],"acknowledgement":"We are grateful to N Barton, F Kondrashov, M Lagator, M Pleska, R Roemhild, D Siekhaus, and G\r\nTkacik for input on the manuscript and to K Tomasek for help with flow cytometry.","type":"journal_article","intvolume":"        11","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"12333","file":[{"date_updated":"2023-01-23T08:56:21Z","file_size":8835954,"access_level":"open_access","checksum":"9321fd5f06ff59d5e2d33daee84b3da1","relation":"main_file","file_id":"12338","success":1,"creator":"dernst","file_name":"2022_eLife_Tomanek.pdf","content_type":"application/pdf","date_created":"2023-01-23T08:56:21Z"}],"quality_controlled":"1","corr_author":"1","ddc":["570"],"has_accepted_license":"1","article_number":"e82240","date_created":"2023-01-22T23:00:55Z","year":"2022","publication":"eLife","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/ELIFE.82240","external_id":{"isi":["000912674700001"],"pmid":["36546673"]},"publication_status":"published","abstract":[{"text":"Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.","lang":"eng"}],"article_processing_charge":"No","title":"Adaptation dynamics between copynumber and point mutations","volume":11,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Tomanek","first_name":"Isabella","full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"related_material":{"record":[{"relation":"research_data","id":"12339","status":"public"}],"link":[{"url":"https://doi.org/10.5281/zenodo.6974122","relation":"software"}]}},{"doi":"10.5061/dryad.rfj6q57ds","status":"public","day":"23","year":"2022","date_created":"2023-01-23T09:00:37Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.rfj6q57ds"}],"ddc":["570"],"corr_author":"1","citation":{"short":"I. Tomanek, C.C. Guet, (2022).","ieee":"I. Tomanek and C. C. Guet, “Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose.” Dryad, 2022.","ama":"Tomanek I, Guet CC. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. 2022. doi:<a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>","ista":"Tomanek I, Guet CC. 2022. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose, Dryad, <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>.","apa":"Tomanek, I., &#38; Guet, C. C. (2022). Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. Dryad. <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">https://doi.org/10.5061/dryad.rfj6q57ds</a>","chicago":"Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.” Dryad, 2022. <a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">https://doi.org/10.5061/dryad.rfj6q57ds</a>.","mla":"Tomanek, Isabella, and Calin C. Guet. <i>Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.5061/dryad.rfj6q57ds\">10.5061/dryad.rfj6q57ds</a>."},"_id":"12339","related_material":{"record":[{"relation":"used_in_publication","id":"12333","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella","last_name":"Tomanek","first_name":"Isabella"},{"last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","month":"12","title":"Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose","date_published":"2022-12-23T00:00:00Z","department":[{"_id":"CaGu"}],"publisher":"Dryad","date_updated":"2025-03-06T14:03:50Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales."}],"oa":1},{"oa":1,"file_date_updated":"2023-02-02T09:39:25Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-06-18T19:57:47Z","language":[{"iso":"eng"}],"month":"09","date_published":"2022-09-22T00:00:00Z","type":"dissertation","oa_version":"Published Version","_id":"12358","project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"citation":{"mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>.","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022."},"ec_funded":1,"day":"22","status":"public","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}],"publication_status":"published","page":"138","article_processing_charge":"No","degree_awarded":"PhD","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","supervisor":[{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J"}],"OA_place":"publisher","author":[{"first_name":"Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"status":"public","id":"8385","relation":"part_of_dissertation"},{"id":"11736","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9818"}]},"acknowledged_ssus":[{"_id":"SSU"}],"file":[{"date_created":"2023-01-25T12:04:41Z","file_name":"thesis_gsperl.pdf","content_type":"application/pdf","creator":"cchlebak","description":"This is the main PDF file of the thesis. File size: 105 MB","file_id":"12371","access_level":"open_access","title":"Thesis","checksum":"083722acbb8115e52e3b0fdec6226769","relation":"main_file","date_updated":"2023-02-02T09:29:57Z","file_size":104497530},{"creator":"cchlebak","date_created":"2023-02-02T09:33:37Z","file_name":"thesis_gsperl_compressed.pdf","content_type":"application/pdf","access_level":"open_access","title":"Thesis (compressed 23MB)","relation":"main_file","checksum":"511f82025e5fcb70bff4731d6896ca07","file_size":23183710,"date_updated":"2023-02-02T09:33:37Z","description":"This version of the thesis uses stronger image compression for a smaller file size of 23MB.","file_id":"12483"},{"file_id":"12484","file_size":98382247,"date_updated":"2023-02-02T09:39:25Z","access_level":"open_access","relation":"source_file","checksum":"ed4cb85225eedff761c25bddfc37a2ed","file_name":"thesis-source.zip","content_type":"application/x-zip-compressed","date_created":"2023-02-02T09:39:25Z","creator":"cchlebak"}],"corr_author":"1","ddc":["000","620"],"has_accepted_license":"1","year":"2022","date_created":"2023-01-24T10:49:46Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]},"doi":"10.15479/at:ista:12103"},{"oa":1,"file_date_updated":"2023-01-25T10:52:46Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"date_updated":"2026-06-18T19:47:50Z","language":[{"iso":"eng"}],"month":"09","date_published":"2022-09-29T00:00:00Z","type":"dissertation","oa_version":"Published Version","_id":"12368","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"citation":{"mla":"Arslan, Feyza N. <i>Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>.","chicago":"Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>.","apa":"Arslan, F. N. (2022). <i>Remodeling of E-cadherin-mediated contacts via cortical  flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12153\">https://doi.org/10.15479/at:ista:12153</a>","ista":"Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria.","ama":"Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12153\">10.15479/at:ista:12153</a>","short":"F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022.","ieee":"F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022."},"ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"29","status":"public","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\u0002mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\u0002cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts.","lang":"eng"}],"publication_status":"published","page":"113","article_processing_charge":"No","degree_awarded":"PhD","title":"Remodeling of E-cadherin-mediated contacts via cortical  flows","supervisor":[{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"OA_place":"publisher","author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan","first_name":"Feyza N"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"id":"9350","relation":"part_of_dissertation","status":"public"}]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"NanoFab"}],"file":[{"date_updated":"2023-01-25T10:52:46Z","file_size":14581024,"checksum":"e54a3e69b83ebf166544164afd25608e","relation":"main_file","access_level":"open_access","file_id":"12369","creator":"cchlebak","success":1,"content_type":"application/pdf","file_name":"THESIS_FINAL_FArslan_pdfa.pdf","date_created":"2023-01-25T10:52:46Z"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","year":"2022","date_created":"2023-01-25T10:43:24Z","doi":"10.15479/at:ista:12153","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-025-1 "]}},{"page":"196","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n"}],"publication_status":"published","degree_awarded":"PhD","title":"Translation-invariant quantum systems with effectively broken symmetry","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"author":[{"first_name":"Morris","last_name":"Brooks","orcid":"0000-0002-6249-0928","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","full_name":"Brooks, Morris"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9005"}]},"corr_author":"1","file":[{"file_id":"12391","checksum":"b31460e937f33b557abb40ebef02b567","relation":"main_file","access_level":"open_access","file_size":3095225,"date_updated":"2023-01-26T10:02:34Z","date_created":"2023-01-26T10:02:34Z","file_name":"Brooks_Thesis.pdf","content_type":"application/pdf","creator":"cchlebak","success":1},{"creator":"cchlebak","content_type":"application/octet-stream","file_name":"Brooks_Thesis.tex","date_created":"2023-01-26T10:02:42Z","date_updated":"2023-01-26T10:02:42Z","file_size":809842,"checksum":"9751869fa5e7981588ad4228f4fd4bd6","relation":"source_file","access_level":"closed","file_id":"12392"}],"has_accepted_license":"1","ddc":["500"],"year":"2022","date_created":"2023-01-26T10:00:42Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:12390","oa":1,"file_date_updated":"2023-01-26T10:02:42Z","language":[{"iso":"eng"}],"month":"12","date_published":"2022-12-15T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_updated":"2026-04-16T08:20:52Z","oa_version":"Published Version","type":"dissertation","_id":"12390","citation":{"mla":"Brooks, Morris. <i>Translation-Invariant Quantum Systems with Effectively Broken Symmetry</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12390\">10.15479/at:ista:12390</a>.","chicago":"Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12390\">https://doi.org/10.15479/at:ista:12390</a>.","apa":"Brooks, M. (2022). <i>Translation-invariant quantum systems with effectively broken symmetry</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12390\">https://doi.org/10.15479/at:ista:12390</a>","ama":"Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12390\">10.15479/at:ista:12390</a>","ista":"Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria.","ieee":"M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022.","short":"M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022."},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"alternative_title":["ISTA Thesis"],"status":"public","day":"15"},{"author":[{"orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige","last_name":"Ishida","first_name":"Sadashige"},{"first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"last_name":"Chern","first_name":"Albert","full_name":"Chern, Albert"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":41,"related_material":{"record":[{"status":"public","id":"20551","relation":"dissertation_contains"}]},"article_processing_charge":"No","external_id":{"isi":["000891651900061"]},"publication_status":"published","abstract":[{"lang":"eng","text":"This paper presents a new representation of curve dynamics, with applications to vortex filaments in fluid dynamics. Instead of representing these filaments with explicit curve geometry and Lagrangian equations of motion, we represent curves implicitly with a new co-dimensional 2 level set description. Our implicit representation admits several redundant mathematical degrees of freedom in both the configuration and the dynamics of the curves, which can be tailored specifically to improve numerical robustness, in contrast to naive approaches for implicit curve dynamics that suffer from overwhelming numerical stability problems. Furthermore, we note how these hidden degrees of freedom perfectly map to a Clebsch representation in fluid dynamics. Motivated by these observations, we introduce untwisted level set functions and non-swirling dynamics which successfully regularize sources of numerical instability, particularly in the twisting modes around curve filaments. A consequence is a novel simulation method which produces stable dynamics for large numbers of interacting vortex filaments and effortlessly handles topological changes and re-connection events."}],"title":"Hidden degrees of freedom in implicit vortex filaments","date_created":"2023-01-29T23:00:59Z","year":"2022","article_number":"241","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"doi":"10.1145/3550454.3555459","issue":"6","publication":"ACM Transactions on Graphics","quality_controlled":"1","file":[{"file_id":"12433","access_level":"open_access","relation":"main_file","checksum":"a2fba257fdefe0e747182be6c0f7c70c","date_updated":"2023-01-30T07:15:48Z","file_size":15551202,"date_created":"2023-01-30T07:15:48Z","content_type":"application/pdf","file_name":"2022_ACM_Ishida.pdf","success":1,"creator":"dernst"}],"has_accepted_license":"1","ddc":["000"],"oa_version":"Published Version","intvolume":"        41","article_type":"original","acknowledgement":"We thank the visual computing group at IST Austria for their valuable discussions and feedback. Houdini Education licenses were provided by SideFX software. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","type":"journal_article","scopus_import":"1","_id":"12431","isi":1,"file_date_updated":"2023-01-30T07:15:48Z","oa":1,"date_published":"2022-12-01T00:00:00Z","language":[{"iso":"eng"}],"month":"12","date_updated":"2026-04-07T12:02:23Z","department":[{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","status":"public","citation":{"mla":"Ishida, Sadashige, et al. “Hidden Degrees of Freedom in Implicit Vortex Filaments.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 6, 241, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3550454.3555459\">10.1145/3550454.3555459</a>.","apa":"Ishida, S., Wojtan, C., &#38; Chern, A. (2022). Hidden degrees of freedom in implicit vortex filaments. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3550454.3555459\">https://doi.org/10.1145/3550454.3555459</a>","chicago":"Ishida, Sadashige, Chris Wojtan, and Albert Chern. “Hidden Degrees of Freedom in Implicit Vortex Filaments.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3550454.3555459\">https://doi.org/10.1145/3550454.3555459</a>.","ama":"Ishida S, Wojtan C, Chern A. Hidden degrees of freedom in implicit vortex filaments. <i>ACM Transactions on Graphics</i>. 2022;41(6). doi:<a href=\"https://doi.org/10.1145/3550454.3555459\">10.1145/3550454.3555459</a>","ista":"Ishida S, Wojtan C, Chern A. 2022. Hidden degrees of freedom in implicit vortex filaments. ACM Transactions on Graphics. 41(6), 241.","short":"S. Ishida, C. Wojtan, A. Chern, ACM Transactions on Graphics 41 (2022).","ieee":"S. Ishida, C. Wojtan, and A. Chern, “Hidden degrees of freedom in implicit vortex filaments,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 6. Association for Computing Machinery, 2022."},"project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}]}]