[{"das_tickbox":"1","_id":"15079","quality_controlled":"1","publication":"Oberwolfach Reports","status":"public","oa_version":"None","month":"11","issue":"4","language":[{"iso":"eng"}],"citation":{"short":"L. Erdös, F. Götze, A. Guionnet, Oberwolfach Reports 16 (2020) 3459–3527.","chicago":"Erdös, László, Friedrich Götze, and Alice Guionnet. “Random Matrices.” Oberwolfach Reports. EMS Press, 2020. https://doi.org/10.4171/owr/2019/56.","ista":"Erdös L, Götze F, Guionnet A. 2020. Random matrices. Oberwolfach Reports. 16(4), 3459–3527.","apa":"Erdös, L., Götze, F., & Guionnet, A. (2020). Random matrices. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2019/56","ama":"Erdös L, Götze F, Guionnet A. Random matrices. Oberwolfach Reports. 2020;16(4):3459-3527. doi:10.4171/owr/2019/56","mla":"Erdös, László, et al. “Random Matrices.” Oberwolfach Reports, vol. 16, no. 4, EMS Press, 2020, pp. 3459–527, doi:10.4171/owr/2019/56.","ieee":"L. Erdös, F. Götze, and A. Guionnet, “Random matrices,” Oberwolfach Reports, vol. 16, no. 4. EMS Press, pp. 3459–3527, 2020."},"doi":"10.4171/owr/2019/56","intvolume":" 16","date_created":"2024-03-05T07:54:44Z","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","text":"Large complex systems tend to develop universal patterns that often represent their essential characteristics. For example, the cumulative effects of independent or weakly dependent random variables often yield the Gaussian universality class via the central limit theorem. For non-commutative random variables, e.g. matrices, the Gaussian behavior is often replaced by another universality class, commonly called random matrix statistics. Nearby eigenvalues are strongly correlated, and, remarkably, their correlation structure is universal, depending only on the symmetry type of the matrix. Even more surprisingly, this feature is not restricted to matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s that distributions of the gaps between energy levels of complicated quantum systems universally follow the same random matrix statistics. This claim has never been rigorously proved for any realistic physical system but experimental data and extensive numerics leave no doubt as to its correctness. Since then random matrices have proved to be extremely useful phenomenological models in a wide range of applications beyond quantum physics that include number theory, statistics, neuroscience, population dynamics, wireless communication and mathematical finance. The ubiquity of random matrices in natural sciences is still a mystery, but recent years have witnessed a breakthrough in the mathematical description of the statistical structure of their spectrum. Random matrices and closely related areas such as log-gases have become an extremely active research area in probability theory.\r\nThis workshop brought together outstanding researchers from a variety of mathematical backgrounds whose areas of research are linked to random matrices. While there are strong links between their motivations, the techniques used by these researchers span a large swath of mathematics, ranging from purely algebraic techniques to stochastic analysis, classical probability theory, operator algebra, supersymmetry, orthogonal polynomials, etc."}],"volume":16,"publisher":"EMS Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-11-19T00:00:00Z","date_updated":"2026-07-06T11:53:24Z","title":"Random matrices","article_processing_charge":"No","year":"2020","publication_status":"published","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Friedrich","last_name":"Götze","full_name":"Götze, Friedrich"},{"full_name":"Guionnet, Alice","last_name":"Guionnet","first_name":"Alice"}],"type":"journal_article","article_type":"original","publication_identifier":{"issn":["1660-8933"]},"day":"19","page":"3459-3527"},{"_id":"8042","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04819"}],"oa_version":"Preprint","quality_controlled":"1","scopus_import":"1","department":[{"_id":"RoSe"}],"volume":22,"citation":{"mla":"Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society, vol. 22, no. 7, EMS Press, 2020, pp. 2331–403, doi:10.4171/JEMS/966.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum of Bose gases interacting through singular potentials,” Journal of the European Mathematical Society, vol. 22, no. 7. EMS Press, pp. 2331–2403, 2020.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 22(7), 2331–2403.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. EMS Press. https://doi.org/10.4171/JEMS/966","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of Bose gases interacting through singular potentials. Journal of the European Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.” Journal of the European Mathematical Society. EMS Press, 2020. https://doi.org/10.4171/JEMS/966.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403."},"doi":"10.4171/JEMS/966","author":[{"full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara","last_name":"Boccato"},{"full_name":"Brennecke, Christian","first_name":"Christian","last_name":"Brennecke"},{"last_name":"Cenatiempo","first_name":"Serena","full_name":"Cenatiempo, Serena"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"date_updated":"2026-07-06T11:53:41Z","title":"The excitation spectrum of Bose gases interacting through singular potentials","article_type":"original","publication_identifier":{"issn":["1435-9855"]},"day":"01","arxiv":1,"external_id":{"arxiv":["1704.04819"],"isi":["000548174700006"]},"issue":"7","das_tickbox":"1","publication":"Journal of the European Mathematical Society","status":"public","month":"07","date_created":"2020-06-29T07:59:35Z","abstract":[{"lang":"eng","text":"We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N."}],"publisher":"EMS Press","language":[{"iso":"eng"}],"intvolume":" 22","article_processing_charge":"No","year":"2020","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-01T00:00:00Z","page":"2331-2403","isi":1,"type":"journal_article","oa":1},{"external_id":{"arxiv":["1906.08463"],"isi":["000596833300001"]},"arxiv":1,"article_type":"original","publication_identifier":{"eissn":["1420-8946"],"issn":["0010-2571"]},"day":"07","date_updated":"2026-07-06T11:54:01Z","title":"Free rational points on smooth hypersurfaces","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D"},{"first_name":"Will","last_name":"Sawin","full_name":"Sawin, Will"}],"citation":{"ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 2020;95(4):635-659. doi:10.4171/CMH/499","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","apa":"Browning, T. D., & Sawin, W. (2020). Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. EMS Press. https://doi.org/10.4171/CMH/499","ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” Commentarii Mathematici Helvetici, vol. 95, no. 4. EMS Press, pp. 635–659, 2020.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” Commentarii Mathematici Helvetici, vol. 95, no. 4, EMS Press, 2020, pp. 635–59, doi:10.4171/CMH/499.","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” Commentarii Mathematici Helvetici. EMS Press, 2020. https://doi.org/10.4171/CMH/499."},"doi":"10.4171/CMH/499","volume":95,"department":[{"_id":"TiBr"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08463"}],"oa_version":"Preprint","quality_controlled":"1","_id":"9007","oa":1,"isi":1,"type":"journal_article","page":"635-659","date_published":"2020-12-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","year":"2020","publication_status":"published","intvolume":" 95","language":[{"iso":"eng"}],"publisher":"EMS Press","abstract":[{"lang":"eng","text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals."}],"date_created":"2021-01-17T23:01:11Z","month":"12","status":"public","publication":"Commentarii Mathematici Helvetici","das_tickbox":"1","issue":"4"},{"date_published":"2020-06-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Organic Chemistry","Biochemistry"],"year":"2020","article_processing_charge":"No","publication_status":"published","type":"journal_article","page":"1357-1417","month":"06","publication":"Oberwolfach Reports","status":"public","das_tickbox":"1","issue":"2","intvolume":" 16","language":[{"iso":"eng"}],"publisher":"EMS Press","abstract":[{"text":"This workshop focused on interactions between the various perspectives on the moduli space of Higgs bundles over a Riemann surface. This subject draws on algebraic geometry, geometric topology, geometric analysis and mathematical physics, and the goal was to promote interactions between these various branches of the subject. The main current directions of research were well represented by the participants, and the talks included many from both senior and junior participants.","lang":"eng"}],"date_created":"2024-03-04T11:36:31Z","date_updated":"2026-07-06T11:52:54Z","title":"Geometry and physics of Higgs bundles","author":[{"full_name":"Anderson, Lara","first_name":"Lara","last_name":"Anderson"},{"first_name":"Tamás","orcid":"0000-0002-9582-2634","last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás"},{"full_name":"Mazzeo, Rafe","last_name":"Mazzeo","first_name":"Rafe"},{"full_name":"Schaposnik, Laura","last_name":"Schaposnik","first_name":"Laura"}],"article_type":"original","publication_identifier":{"issn":["1660-8933"]},"day":"04","oa_version":"None","quality_controlled":"1","_id":"15070","citation":{"chicago":"Anderson, Lara, Tamás Hausel, Rafe Mazzeo, and Laura Schaposnik. “Geometry and Physics of Higgs Bundles.” Oberwolfach Reports. EMS Press, 2020. https://doi.org/10.4171/owr/2019/23.","short":"L. Anderson, T. Hausel, R. Mazzeo, L. Schaposnik, Oberwolfach Reports 16 (2020) 1357–1417.","mla":"Anderson, Lara, et al. “Geometry and Physics of Higgs Bundles.” Oberwolfach Reports, vol. 16, no. 2, EMS Press, 2020, pp. 1357–417, doi:10.4171/owr/2019/23.","ieee":"L. Anderson, T. Hausel, R. Mazzeo, and L. Schaposnik, “Geometry and physics of Higgs bundles,” Oberwolfach Reports, vol. 16, no. 2. EMS Press, pp. 1357–1417, 2020.","apa":"Anderson, L., Hausel, T., Mazzeo, R., & Schaposnik, L. (2020). Geometry and physics of Higgs bundles. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2019/23","ista":"Anderson L, Hausel T, Mazzeo R, Schaposnik L. 2020. Geometry and physics of Higgs bundles. Oberwolfach Reports. 16(2), 1357–1417.","ama":"Anderson L, Hausel T, Mazzeo R, Schaposnik L. Geometry and physics of Higgs bundles. Oberwolfach Reports. 2020;16(2):1357-1417. doi:10.4171/owr/2019/23"},"doi":"10.4171/owr/2019/23","volume":16,"department":[{"_id":"TaHa"}]},{"citation":{"ieee":"C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,” Oberwolfach Reports, vol. 16, no. 3. EMS Press, pp. 2541–2603, 2020.","mla":"Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports, vol. 16, no. 3, EMS Press, 2020, pp. 2541–603, doi:10.4171/owr/2019/41.","ama":"Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach Reports. 2020;16(3):2541-2603. doi:10.4171/owr/2019/41","ista":"Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems. Oberwolfach Reports. 16(3), 2541–2603.","apa":"Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2020). Many-body quantum systems. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2019/41","chicago":"Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel. “Many-Body Quantum Systems.” Oberwolfach Reports. EMS Press, 2020. https://doi.org/10.4171/owr/2019/41.","short":"C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020) 2541–2603."},"doi":"10.4171/owr/2019/41","intvolume":" 16","language":[{"iso":"eng"}],"publisher":"EMS Press","volume":16,"date_created":"2024-03-04T11:46:12Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"The interaction among fundamental particles in nature leads to many interesting effects in quantum statistical mechanics; examples include superconductivity for charged systems and superfluidity in cold gases. It is a huge challenge for mathematical physics to understand the collective behavior of systems containing a large number of particles, emerging from known microscopic interactions. In this workshop we brought together researchers working on different aspects of many-body quantum mechanics to discuss recent developments, exchange ideas and propose new challenges and research directions.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","status":"public","publication":"Oberwolfach Reports","month":"09","_id":"15072","das_tickbox":"1","issue":"3","type":"journal_article","page":"2541-2603","day":"10","article_type":"original","publication_identifier":{"issn":["1660-8933"]},"title":"Many-body quantum systems","date_published":"2020-09-10T00:00:00Z","date_updated":"2026-07-06T11:53:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"},{"last_name":"Warzel","first_name":"Simone","full_name":"Warzel, Simone"}],"publication_status":"published","year":"2020","article_processing_charge":"No"},{"date_published":"2020-10-21T00:00:00Z","article_number":"138","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-12-28T08:24:08Z","success":1,"file_id":"8976","file_size":696653,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-12-28T08:24:08Z","checksum":"d75359b9814e78d57c0a481b7cde3751","creator":"dernst","file_name":"2020_ElectronJProbab_Redig.pdf"}],"year":"2020","article_processing_charge":"No","publication_status":"published","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","publication":"Electronic Journal of Probability","status":"public","month":"10","ddc":["510"],"das_tickbox":"1","intvolume":" 25","language":[{"iso":"eng"}],"publisher":"Institute of Mathematical Statistics","date_created":"2020-12-27T23:01:17Z","has_accepted_license":"1","abstract":[{"text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity.","lang":"eng"}],"date_updated":"2026-07-06T12:04:40Z","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","author":[{"last_name":"Redig","first_name":"Frank","full_name":"Redig, Frank"},{"last_name":"Saada","first_name":"Ellen","full_name":"Saada, Ellen"},{"full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico","last_name":"Sau"}],"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"arxiv":1,"acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","article_type":"original","file_date_updated":"2020-12-28T08:24:08Z","publication_identifier":{"eissn":["1083-6489"]},"day":"21","oa_version":"Published Version","quality_controlled":"1","_id":"8973","citation":{"short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020."},"doi":"10.1214/20-EJP536","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"volume":25,"scopus_import":"1","department":[{"_id":"JaMa"}]},{"page":"9220-9230","type":"journal_article","isi":1,"year":"2020","article_processing_charge":"No","publication_status":"published","date_published":"2020-05-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Chemical Society","date_created":"2020-06-29T07:59:35Z","abstract":[{"lang":"eng","text":"The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I."}],"pmid":1,"intvolume":" 142","language":[{"iso":"eng"}],"issue":"20","corr_author":"1","publication":"Journal of the American Chemical Society","status":"public","month":"05","related_material":{"record":[{"relation":"research_data","id":"9878","status":"public"},{"relation":"research_data","id":"9326","status":"public"},{"relation":"research_data","id":"9713","status":"public"}]},"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"article_type":"original","day":"20","external_id":{"pmid":["32347721"],"isi":["000537415600020"]},"author":[{"last_name":"Gupta","first_name":"Chitrak","full_name":"Gupta, Chitrak"},{"first_name":"Umesh","last_name":"Khaniya","full_name":"Khaniya, Umesh"},{"first_name":"Chun Kit","last_name":"Chan","full_name":"Chan, Chun Kit"},{"last_name":"Dehez","first_name":"Francois","full_name":"Dehez, Francois"},{"full_name":"Shekhar, Mrinal","last_name":"Shekhar","first_name":"Mrinal"},{"last_name":"Gunner","first_name":"M. R.","full_name":"Gunner, M. R."},{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"full_name":"Singharoy, Abhishek","first_name":"Abhishek","last_name":"Singharoy"}],"date_updated":"2026-07-06T12:16:34Z","title":"Charge transfer and chemo-mechanical coupling in respiratory complex I","volume":142,"scopus_import":"1","department":[{"_id":"LeSa"}],"doi":"10.1021/jacs.9b13450","citation":{"chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.","short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142 (2020) 9220–9230.","mla":"Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of the American Chemical Society, vol. 142, no. 20, American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450.","ieee":"C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I,” Journal of the American Chemical Society, vol. 142, no. 20. American Chemical Society, pp. 9220–9230, 2020.","ama":"Gupta C, Khaniya U, Chan CK, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230. doi:10.1021/jacs.9b13450","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. 142(20), 9220–9230.","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b13450"},"oa_version":"None","quality_controlled":"1","_id":"8040"},{"year":"2020","article_processing_charge":"No","publication_status":"published","date_published":"2020-01-08T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"669-676","oa":1,"type":"journal_article","isi":1,"issue":"1","ddc":["570"],"month":"01","publication":"Nano Letters","status":"public","corr_author":"1","publisher":"American Chemical Society","pmid":1,"abstract":[{"lang":"eng","text":"In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors."}],"date_created":"2019-12-10T15:36:05Z","intvolume":" 20","language":[{"iso":"eng"}],"author":[{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217"},{"full_name":"Lipowsky, Reinhard","first_name":"Reinhard","last_name":"Lipowsky"}],"date_updated":"2026-07-06T12:14:33Z","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","article_type":"letter_note","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"9726"},{"id":"9885","relation":"research_data","status":"public"}]},"day":"08","external_id":{"pmid":["31797672"],"isi":["000507151600087"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.nanolett.9b04445"}],"oa_version":"Published Version","quality_controlled":"1","_id":"7166","volume":20,"scopus_import":"1","department":[{"_id":"EdHa"}],"citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20, no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445.","ieee":"M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors is determined by strain-induced unbinding,” Nano Letters, vol. 20, no. 1. American Chemical Society, pp. 669–676, 2020.","ama":"Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 2020;20(1):669-676. doi:10.1021/acs.nanolett.9b04445","apa":"Ucar, M. C., & Lipowsky, R. (2020). Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445","ista":"Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676."},"doi":"10.1021/acs.nanolett.9b04445"},{"doi":"10.1021/jacs.9b13450.s001","citation":{"short":"C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020).","chicago":"Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s001.","ama":"Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001","apa":"Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s001","ista":"Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society, 10.1021/jacs.9b13450.s001.","mla":"Gupta, Chitrak, et al. Supporting Information. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s001.","ieee":"C. Gupta et al., “Supporting information.” American Chemical Society, 2020."},"department":[{"_id":"LeSa"}],"abstract":[{"text":"Additional analyses of the trajectories","lang":"eng"}],"date_created":"2021-07-23T12:02:39Z","publisher":"American Chemical Society","_id":"9713","oa_version":"Published Version","status":"public","month":"05","type":"research_data_reference","day":"20","related_material":{"record":[{"id":"8040","relation":"used_in_publication","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Supporting information","date_published":"2020-05-20T00:00:00Z","date_updated":"2026-07-06T12:16:34Z","article_processing_charge":"No","year":"2020","author":[{"last_name":"Gupta","first_name":"Chitrak","full_name":"Gupta, Chitrak"},{"full_name":"Khaniya, Umesh","last_name":"Khaniya","first_name":"Umesh"},{"last_name":"Chan","first_name":"Chun Kit","full_name":"Chan, Chun Kit"},{"first_name":"Francois","last_name":"Dehez","full_name":"Dehez, Francois"},{"full_name":"Shekhar, Mrinal","first_name":"Mrinal","last_name":"Shekhar"},{"full_name":"Gunner, M.R.","first_name":"M.R.","last_name":"Gunner"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"last_name":"Singharoy","first_name":"Abhishek","full_name":"Singharoy, Abhishek"}]},{"_id":"9885","status":"public","oa_version":"Published Version","month":"01","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society, 2020, doi:10.1021/acs.nanolett.9b04445.s002.","ieee":"M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society, 2020.","ista":"Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society, 10.1021/acs.nanolett.9b04445.s002.","ama":"Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002","apa":"Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445.s002","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.","short":"M.C. Ucar, R. Lipowsky, (2020)."},"doi":"10.1021/acs.nanolett.9b04445.s002","date_created":"2021-08-11T13:16:03Z","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)"}],"publisher":"American Chemical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-01-08T00:00:00Z","date_updated":"2026-07-06T12:14:33Z","title":"MURL_Dataz","year":"2020","article_processing_charge":"No","author":[{"orcid":"0000-0003-0506-4217","last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","first_name":"Reinhard","last_name":"Lipowsky"}],"type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","id":"7166","status":"public"}]},"day":"08"},{"project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020."},"doi":"10.15479/AT:ISTA:8155","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"8155","oa_version":"Published Version","OA_place":"publisher","day":"24","file_date_updated":"2020-07-30T13:04:55Z","related_material":{"record":[{"id":"7569","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7652","relation":"part_of_dissertation"},{"status":"public","id":"7675","relation":"part_of_dissertation"}]},"acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","publication_identifier":{"issn":["2663-337X"]},"title":"Gene regulation across scales – how biophysical constraints shape evolution","date_updated":"2026-07-06T12:43:42Z","author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"date_created":"2020-07-23T09:51:28Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. "}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","corr_author":"1","ddc":["530","570"],"status":"public","month":"07","degree_awarded":"PhD","type":"dissertation","oa":1,"page":"310","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-07-24T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2020","file":[{"date_updated":"2020-07-27T12:00:07Z","success":1,"file_id":"8176","access_level":"open_access","content_type":"application/pdf","file_size":16638998,"file_name":"Thesis_RokGrah_200727_convertedNew.pdf","creator":"rgrah","date_created":"2020-07-27T12:00:07Z","relation":"main_file"},{"date_updated":"2020-07-30T13:04:55Z","file_id":"8177","access_level":"closed","content_type":"application/zip","file_size":347459978,"creator":"rgrah","file_name":"Thesis_new.zip","date_created":"2020-07-27T12:02:23Z","relation":"main_file"}]},{"author":[{"first_name":"Rok","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","article_processing_charge":"No","publication_status":"published","date_updated":"2026-07-06T12:43:43Z","date_published":"2020-04-09T00:00:00Z","title":"Normative models of enhancer function","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"8155","relation":"dissertation_contains","status":"public"}]},"day":"09","external_id":{"biorxivid":["10.1101/2020.04.08.029405"]},"oa":1,"type":"preprint","biorxivid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"publication":"bioRxiv","status":"public","month":"04","corr_author":"1","oa_version":"Preprint","das_tickbox":"1","_id":"7675","date_created":"2020-04-23T10:12:51Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology."}],"citation":{"mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, 2020, doi:10.1101/2020.04.08.029405.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. 2020.","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. https://doi.org/10.1101/2020.04.08.029405","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv, 2020. https://doi.org/10.1101/2020.04.08.029405.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020)."},"doi":"10.1101/2020.04.08.029405","project":[{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"language":[{"iso":"eng"}]},{"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","date_published":"2020-11-05T00:00:00Z","date_updated":"2026-07-06T12:45:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Santini, Laura","first_name":"Laura","last_name":"Santini"},{"full_name":"Halbritter, Florian","first_name":"Florian","last_name":"Halbritter"},{"full_name":"Titz-Teixeira, Fabian","first_name":"Fabian","last_name":"Titz-Teixeira"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"first_name":"Andreas","last_name":"Lackner","full_name":"Lackner, Andreas"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Laue, Ernest","first_name":"Ernest","last_name":"Laue"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"first_name":"Andreas","last_name":"Beyer","full_name":"Beyer, Andreas"},{"full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F.","last_name":"Perry"},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"}],"publication_status":"submitted","article_processing_charge":"No","year":"2020","oa":1,"external_id":{"pmid":["PPR234457 "]},"type":"preprint","day":"05","publication":"bioRxiv","month":"11","status":"public","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"_id":"8813","das_tickbox":"1","doi":"10.1101/2020.11.03.366948","citation":{"apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. https://doi.org/10.1101/2020.11.03.366948","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948.","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. .","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, doi:10.1101/2020.11.03.366948.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, n.d. https://doi.org/10.1101/2020.11.03.366948."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation."}],"pmid":1,"department":[{"_id":"SiHi"}],"date_created":"2020-11-26T07:17:19Z"},{"type":"preprint","oa":1,"day":"19","page":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-02-19T00:00:00Z","date_updated":"2026-07-06T12:53:37Z","title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","article_processing_charge":"No","year":"2020","publication_status":"published","author":[{"last_name":"Wei","first_name":"Zhuang","full_name":"Wei, Zhuang"},{"first_name":"Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Liu","first_name":"Tao","full_name":"Liu, Tao"},{"last_name":"Wu","first_name":"Yuan","full_name":"Wu, Yuan"},{"full_name":"Lei, Ji-Gang","last_name":"Lei","first_name":"Ji-Gang"},{"full_name":"Chen, ZhengJun","first_name":"ZhengJun","last_name":"Chen"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong-Wei","first_name":"Hong-Wei","last_name":"Xue"},{"last_name":"Liao","first_name":"Kan","full_name":"Liao, Kan"}],"language":[{"iso":"eng"}],"doi":"10.1101/791137","citation":{"mla":"Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” BioRxiv, 2020, doi:10.1101/791137.","ieee":"Z. Wei et al., “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” bioRxiv. 2020.","ama":"Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv. 2020. doi:10.1101/791137","ista":"Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv, 10.1101/791137.","apa":"Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020). Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv. https://doi.org/10.1101/791137","chicago":"Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen, Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” BioRxiv, 2020. https://doi.org/10.1101/791137.","short":"Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020)."},"date_created":"2020-03-21T16:34:42Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals."}],"das_tickbox":"1","_id":"7601","main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"month":"02","oa_version":"Preprint","publication":"bioRxiv","status":"public"},{"oa":1,"isi":1,"type":"journal_article","page":"663-671","date_published":"2020-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","year":"2020","publication_status":"published","intvolume":" 53","language":[{"iso":"eng"}],"publisher":"Societe Mathematique de France","date_created":"2020-09-20T22:01:38Z","abstract":[{"lang":"eng","text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions."},{"text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. ","lang":"fre"}],"month":"06","publication":"Annales Scientifiques de l'Ecole Normale Superieure","status":"public","das_tickbox":"1","issue":"3","external_id":{"isi":["000592182600004"],"arxiv":["1708.08013"]},"arxiv":1,"publication_identifier":{"issn":["0012-9593"]},"article_type":"original","day":"01","date_updated":"2026-07-06T13:57:35Z","title":"On the K-theory stable bases of the springer resolution","author":[{"full_name":"Su, C.","first_name":"C.","last_name":"Su"},{"last_name":"Zhao","orcid":"0000-0001-7361-2882","first_name":"Gufang","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhong, C.","first_name":"C.","last_name":"Zhong"}],"citation":{"ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 2020;53(3):663-671. doi:10.24033/asens.2431","apa":"Su, C., Zhao, G., & Zhong, C. (2020). On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. Societe Mathematique de France. https://doi.org/10.24033/asens.2431","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3. Societe Mathematique de France, pp. 663–671, 2020.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure, vol. 53, no. 3, Societe Mathematique de France, 2020, pp. 663–71, doi:10.24033/asens.2431.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” Annales Scientifiques de l’Ecole Normale Superieure. Societe Mathematique de France, 2020. https://doi.org/10.24033/asens.2431."},"doi":"10.24033/asens.2431","volume":53,"scopus_import":"1","department":[{"_id":"TaHa"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"quality_controlled":"1","oa_version":"Preprint","_id":"8539"},{"keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"article_processing_charge":"No","year":"2020","publication_status":"published","date_published":"2020-02-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"605-622","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"issue":"1","status":"public","publication":"SIAM Journal on Mathematical Analysis","corr_author":"1","month":"02","ddc":["510"],"das_tickbox":"1","publisher":"Society for Industrial and Applied Mathematics","date_created":"2021-08-06T07:34:16Z","has_accepted_license":"1","abstract":[{"text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum.","lang":"eng"}],"intvolume":" 52","language":[{"iso":"eng"}],"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli","first_name":"Dario"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"date_updated":"2026-07-06T14:02:25Z","title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","arxiv":1,"article_type":"original","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9733"}]},"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"day":"12","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.08647"}],"oa_version":"Preprint","quality_controlled":"1","_id":"9781","volume":52,"scopus_import":"1","department":[{"_id":"RoSe"}],"doi":"10.1137/19m126284x","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 2020;52(1):605-622. doi:10.1137/19m126284x","apa":"Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19m126284x","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial and Applied Mathematics, pp. 605–622, 2020.","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial and Applied Mathematics, 2020, pp. 605–22, doi:10.1137/19m126284x.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19m126284x."},"project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}]},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8587"},{"status":"public","id":"1120","relation":"part_of_dissertation"},{"status":"public","id":"5886","relation":"part_of_dissertation"}]},"file_date_updated":"2020-12-30T07:18:03Z","publication_identifier":{"issn":["2663-337X"]},"day":"21","OA_place":"publisher","author":[{"first_name":"Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Xiang"}],"date_updated":"2026-07-07T05:31:09Z","title":"Rotation of coupled cold molecules in the presence of a many-body environment","department":[{"_id":"MiLe"}],"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958."},"doi":"10.15479/AT:ISTA:8958","_id":"8958","oa_version":"Published Version","page":"125","ec_funded":1,"type":"dissertation","oa":1,"year":"2020","article_processing_charge":"No","publication_status":"published","file":[{"file_size":3622305,"access_level":"open_access","content_type":"application/pdf","date_created":"2020-12-22T10:55:56Z","relation":"main_file","file_name":"THESIS_Xiang_Li.pdf","checksum":"3994c54a1241451d561db1d4f43bad30","creator":"xli","date_updated":"2020-12-22T10:55:56Z","success":1,"file_id":"8967"},{"file_id":"8968","date_updated":"2020-12-30T07:18:03Z","checksum":"0954ecfc5554c05615c14de803341f00","file_name":"THESIS_Xiang_Li.zip","creator":"xli","date_created":"2020-12-22T10:56:03Z","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_size":4018859}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2020-12-21T00:00:00Z","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"date_created":"2020-12-21T09:44:30Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"}],"language":[{"iso":"eng"}],"degree_awarded":"PhD","status":"public","month":"12","corr_author":"1","ddc":["539"]},{"license":"https://creativecommons.org/licenses/by/3.0/","conference":{"start_date":"2020-10-12","location":"Virtual","name":"DISC: Symposium on Distributed Computing","end_date":"2020-10-16"},"external_id":{"arxiv":["2005.07761"]},"file_date_updated":"2024-03-05T07:08:27Z","related_material":{"record":[{"relation":"later_version","id":"9678","status":"public"}]},"day":"07","arxiv":1,"date_updated":"2026-07-07T06:21:32Z","title":"Brief announcement: Efficient load-balancing through distributed token dropping","author":[{"full_name":"Brandt, Sebastian","first_name":"Sebastian","last_name":"Brandt"},{"first_name":"Barbara","last_name":"Keller","full_name":"Keller, Barbara"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646"},{"last_name":"Suomela","first_name":"Jukka","full_name":"Suomela, Jukka"},{"full_name":"Uitto, Jara","first_name":"Jara","last_name":"Uitto"}],"citation":{"short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” In 34th International Symposium on Distributed Computing, Vol. 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement: Efficient load-balancing through distributed token dropping. 34th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 179, 40.","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020). Brief announcement: Efficient load-balancing through distributed token dropping. In 34th International Symposium on Distributed Computing (Vol. 179). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Brief announcement: Efficient load-balancing through distributed token dropping. In: 34th International Symposium on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement: Efficient load-balancing through distributed token dropping,” in 34th International Symposium on Distributed Computing, Virtual, 2020, vol. 179.","mla":"Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through Distributed Token Dropping.” 34th International Symposium on Distributed Computing, vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40."},"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png"},"doi":"10.4230/LIPIcs.DISC.2020.40","scopus_import":"1","department":[{"_id":"DaAl"}],"volume":179,"_id":"15074","oa_version":"Published Version","quality_controlled":"1","type":"conference","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-10-07T00:00:00Z","article_number":"40","year":"2020","article_processing_charge":"No","publication_status":"published","file":[{"relation":"main_file","date_created":"2024-03-05T07:08:27Z","creator":"dernst","file_name":"2020_LIPIcs_Brandt.pdf","checksum":"23e2d9321aef53092dc1e24a8ab82d72","file_size":303529,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"15075","date_updated":"2024-03-05T07:08:27Z"}],"language":[{"iso":"eng"}],"intvolume":" 179","alternative_title":["LIPIcs"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds."}],"date_created":"2024-03-05T07:09:12Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"status":"public","publication":"34th International Symposium on Distributed Computing","corr_author":"1","month":"10"},{"type":"conference","oa":1,"page":"5533-5543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-12T00:00:00Z","article_processing_charge":"No","year":"2020","file":[{"file_size":741899,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-05-25T09:51:36Z","relation":"main_file","checksum":"2aaaa7d7226e49161311d91627cf783b","creator":"kschuh","file_name":"2020_PMLR_Kurtz.pdf","date_updated":"2021-05-25T09:51:36Z","success":1,"file_id":"9421"}],"language":[{"iso":"eng"}],"intvolume":" 119","date_created":"2021-05-23T22:01:45Z","abstract":[{"lang":"eng","text":"Optimizing convolutional neural networks for fast inference has recently become an extremely active area of research. One of the go-to solutions in this context is weight pruning, which aims to reduce computational and memory footprint by removing large subsets of the connections in a neural network. Surprisingly, much less attention has been given to exploiting sparsity in the activation maps, which tend to be naturally sparse in many settings thanks to the structure of rectified linear (ReLU) activation functions. In this paper, we present an in-depth analysis of methods for maximizing the sparsity of the activations in a trained neural network, and show that, when coupled with an efficient sparse-input convolution algorithm, we can leverage this sparsity for significant performance gains. To induce highly sparse activation maps without accuracy loss, we introduce a new regularization technique, coupled with a new threshold-based sparsification method based on a parameterized activation function called Forced-Activation-Threshold Rectified Linear Unit (FATReLU). We examine the impact of our methods on popular image classification models, showing that most architectures can adapt to significantly sparser activation maps without any accuracy loss. Our second contribution is showing that these these compression gains can be translated into inference speedups: we provide a new algorithm to enable fast convolution operations over networks with sparse activations, and show that it can enable significant speedups for end-to-end inference on a range of popular models on the large-scale ImageNet image classification task on modern Intel CPUs, with little or no retraining cost. "}],"has_accepted_license":"1","das_tickbox":"1","status":"public","publication":"37th International Conference on Machine Learning","ddc":["000"],"month":"07","conference":{"start_date":"2020-07-12","name":"ICML: International Conference on Machine Learning","location":"Online","end_date":"2020-07-18"},"publication_identifier":{"issn":["2640-3498"]},"file_date_updated":"2021-05-25T09:51:36Z","day":"12","date_updated":"2026-07-07T13:42:32Z","title":"Inducing and exploiting activation sparsity for fast neural network inference","author":[{"full_name":"Kurtz, Mark","last_name":"Kurtz","first_name":"Mark"},{"last_name":"Kopinsky","first_name":"Justin","full_name":"Kopinsky, Justin"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"full_name":"Carr, John","last_name":"Carr","first_name":"John"},{"full_name":"Goin, Michael","first_name":"Michael","last_name":"Goin"},{"full_name":"Leiserson, William","first_name":"William","last_name":"Leiserson"},{"full_name":"Moore, Sage","first_name":"Sage","last_name":"Moore"},{"full_name":"Nell, Bill","last_name":"Nell","first_name":"Bill"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"}],"citation":{"mla":"Kurtz, Mark, et al. “Inducing and Exploiting Activation Sparsity for Fast Neural Network Inference.” 37th International Conference on Machine Learning, vol. 119, 2020, pp. 5533–43.","ieee":"M. Kurtz et al., “Inducing and exploiting activation sparsity for fast neural network inference,” in 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5533–5543.","ama":"Kurtz M, Kopinsky J, Gelashvili R, et al. Inducing and exploiting activation sparsity for fast neural network inference. In: 37th International Conference on Machine Learning. Vol 119. ; 2020:5533-5543.","ista":"Kurtz M, Kopinsky J, Gelashvili R, Matveev A, Carr J, Goin M, Leiserson W, Moore S, Nell B, Shavit N, Alistarh D-A. 2020. Inducing and exploiting activation sparsity for fast neural network inference. 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5533–5543.","apa":"Kurtz, M., Kopinsky, J., Gelashvili, R., Matveev, A., Carr, J., Goin, M., … Alistarh, D.-A. (2020). Inducing and exploiting activation sparsity for fast neural network inference. In 37th International Conference on Machine Learning (Vol. 119, pp. 5533–5543). Online.","chicago":"Kurtz, Mark, Justin Kopinsky, Rati Gelashvili, Alexander Matveev, John Carr, Michael Goin, William Leiserson, et al. “Inducing and Exploiting Activation Sparsity for Fast Neural Network Inference.” In 37th International Conference on Machine Learning, 119:5533–43, 2020.","short":"M. Kurtz, J. Kopinsky, R. Gelashvili, A. Matveev, J. Carr, M. Goin, W. Leiserson, S. Moore, B. Nell, N. Shavit, D.-A. Alistarh, in:, 37th International Conference on Machine Learning, 2020, pp. 5533–5543."},"department":[{"_id":"DaAl"}],"scopus_import":"1","volume":119,"_id":"9415","quality_controlled":"1","oa_version":"Published Version"},{"supplementarymaterial":"yes","publisher":"American Physical Society","pmid":1,"date_created":"2020-08-24T06:24:04Z","abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"intvolume":" 125","language":[{"iso":"eng"}],"issue":"4","publication":"Physical Review Letters","status":"public","month":"07","das_tickbox":"0","oa":1,"type":"journal_article","isi":1,"year":"2020","article_processing_charge":"No","publication_status":"published","article_number":"043202","date_published":"2020-07-24T00:00:00Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","volume":125,"department":[{"_id":"OnHo"}],"scopus_import":"1","doi":"10.1103/PhysRevLett.125.043202","citation":{"ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020)."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"quality_controlled":"1","oa_version":"Preprint","_id":"8285","arxiv":1,"acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_type":"original","day":"24","external_id":{"pmid":["32794788"],"arxiv":["1912.10218"],"isi":["000552227400008"]},"author":[{"full_name":"Malia, Benjamin K.","first_name":"Benjamin K.","last_name":"Malia"},{"full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón","first_name":"Julián"},{"last_name":"Wu","first_name":"Yunfan","full_name":"Wu, Yunfan"},{"orcid":"0000-0002-2031-204X","last_name":"Hosten","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur"},{"first_name":"Mark A.","last_name":"Kasevich","full_name":"Kasevich, Mark A."}],"date_updated":"2026-07-08T08:56:44Z","researchdata_availability":"no","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit"}]