[{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1807.08801"}],"publisher":"Society for Industrial & Applied Mathematics","_id":"22080","mathsc":["35Q55","35Q51","35Q82"],"type":"journal_article","intvolume":" 52","doi":"10.1137/19m1265314","author":[{"last_name":"Angelopoulos","first_name":"Yannis","full_name":"Angelopoulos, Yannis"},{"last_name":"Killip","first_name":"Rowan","full_name":"Killip, Rowan"},{"full_name":"Visan, Monica","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","last_name":"Visan","first_name":"Monica"}],"date_created":"2026-06-19T08:26:32Z","month":"01","extern":"1","OA_place":"repository","day":"01","external_id":{"arxiv":["1807.08801"]},"oa_version":"Preprint","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"We consider discrete analogues of two well-known open problems regarding invariant measures for dispersive PDE, namely, the invariance of the Gibbs measure for the continuum (classical) Heisenberg model and the invariance of white noise under focusing cubic nonlinear Schrödinger equation. These continuum models are completely integrable and connected by the Hasimoto transform; correspondingly, we focus our attention on discretizations that are also completely integrable and also connected by a discrete Hasimoto transform. We consider these models on the infinite lattice ℤ. Concretely, for a completely integrable variant of the classical Heisenberg spin chain model (introduced independently by Haldane, Ishimori, and Sklyanin) we prove the existence and uniqueness of solutions for initial data following a Gibbs law (which we show is unique) and show that the Gibbs measure is preserved under these dynamics. In the setting of the focusing Ablowitz--Ladik system, we prove invariance of a measure that we will show is the appropriate discrete analogue of white noise. We also include a thorough discussion of the Poisson geometry associated to the discrete Hasimoto transform introduced by Ishimori that connects the two models studied in this article."}],"oa":1,"year":"2020","volume":52,"date_published":"2020-01-01T00:00:00Z","arxiv":1,"OA_type":"green","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"date_updated":"2026-06-30T12:21:20Z","title":"Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation","issue":"1","scopus_import":"1","publication":"SIAM Journal on Mathematical Analysis","citation":{"short":"Y. Angelopoulos, R. Killip, M. Vişan, SIAM Journal on Mathematical Analysis 52 (2020) 135–163.","mla":"Angelopoulos, Yannis, et al. “Invariant Measures for Integrable Spin Chains and an Integrable Discrete Nonlinear Schrödinger Equation.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2020, pp. 135–63, doi:10.1137/19m1265314.","ista":"Angelopoulos Y, Killip R, Vişan M. 2020. Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation. SIAM Journal on Mathematical Analysis. 52(1), 135–163.","chicago":"Angelopoulos, Yannis, Rowan Killip, and Monica Vişan. “Invariant Measures for Integrable Spin Chains and an Integrable Discrete Nonlinear Schrödinger Equation.” SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics, 2020. https://doi.org/10.1137/19m1265314.","ieee":"Y. Angelopoulos, R. Killip, and M. Vişan, “Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 135–163, 2020.","apa":"Angelopoulos, Y., Killip, R., & Vişan, M. (2020). Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation. SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/19m1265314","ama":"Angelopoulos Y, Killip R, Vişan M. Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation. SIAM Journal on Mathematical Analysis. 2020;52(1):135-163. doi:10.1137/19m1265314"},"page":"135-163","status":"public","das_tickbox":"1"},{"department":[{"_id":"RoSe"}],"issue":"7","publication":"Journal of the European Mathematical Society","page":"2331-2403","citation":{"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.","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","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403.","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.","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.","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."},"scopus_import":"1","isi":1,"das_tickbox":"1","status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","title":"The excitation spectrum of Bose gases interacting through singular potentials","publication_identifier":{"issn":["1435-9855"]},"date_updated":"2026-07-06T11:53:41Z","month":"07","external_id":{"arxiv":["1704.04819"],"isi":["000548174700006"]},"oa_version":"Preprint","day":"01","article_type":"original","publication_status":"published","abstract":[{"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.","lang":"eng"}],"arxiv":1,"oa":1,"year":"2020","date_published":"2020-07-01T00:00:00Z","volume":22,"_id":"8042","main_file_link":[{"url":"https://arxiv.org/abs/1704.04819","open_access":"1"}],"publisher":"EMS Press","type":"journal_article","intvolume":" 22","date_created":"2020-06-29T07:59:35Z","author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara","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"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"}],"doi":"10.4171/JEMS/966"},{"issue":"4","department":[{"_id":"TiBr"}],"status":"public","das_tickbox":"1","scopus_import":"1","isi":1,"publication":"Commentarii Mathematici Helvetici","citation":{"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.","ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 2020;95(4):635-659. doi:10.4171/CMH/499","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","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","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.","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."},"page":"635-659","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1420-8946"],"issn":["0010-2571"]},"date_updated":"2026-07-06T11:54:01Z","title":"Free rational points on smooth hypersurfaces","article_processing_charge":"No","day":"07","external_id":{"arxiv":["1906.08463"],"isi":["000596833300001"]},"oa_version":"Preprint","month":"12","year":"2020","oa":1,"date_published":"2020-12-07T00:00:00Z","volume":95,"arxiv":1,"article_type":"original","publication_status":"published","abstract":[{"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.","lang":"eng"}],"publisher":"EMS Press","main_file_link":[{"url":"https://arxiv.org/abs/1906.08463","open_access":"1"}],"_id":"9007","doi":"10.4171/CMH/499","date_created":"2021-01-17T23:01:11Z","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"full_name":"Sawin, Will","first_name":"Will","last_name":"Sawin"}],"type":"journal_article","intvolume":" 95"},{"quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"138","article_processing_charge":"No","publication_identifier":{"eissn":["1083-6489"]},"date_updated":"2026-07-06T12:04:40Z","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).","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","department":[{"_id":"JaMa"}],"ddc":["510"],"scopus_import":"1","isi":1,"publication":"Electronic Journal of Probability","citation":{"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.","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","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.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","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.","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"},"status":"public","das_tickbox":"1","publisher":"Institute of Mathematical Statistics","_id":"8973","file":[{"file_id":"8976","checksum":"d75359b9814e78d57c0a481b7cde3751","relation":"main_file","success":1,"file_size":696653,"access_level":"open_access","content_type":"application/pdf","file_name":"2020_ElectronJProbab_Redig.pdf","date_created":"2020-12-28T08:24:08Z","creator":"dernst","date_updated":"2020-12-28T08:24:08Z"}],"intvolume":" 25","type":"journal_article","doi":"10.1214/20-EJP536","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"date_created":"2020-12-27T23:01:17Z","author":[{"last_name":"Redig","first_name":"Frank","full_name":"Redig, Frank"},{"last_name":"Saada","first_name":"Ellen","full_name":"Saada, Ellen"},{"last_name":"Sau","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico"}],"month":"10","has_accepted_license":"1","day":"21","ec_funded":1,"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"oa_version":"Published Version","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"file_date_updated":"2020-12-28T08:24:08Z","year":"2020","oa":1,"date_published":"2020-10-21T00:00:00Z","volume":25,"arxiv":1},{"type":"journal_article","intvolume":" 20","date_created":"2019-12-10T15:36:05Z","author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","last_name":"Ucar","first_name":"Mehmet C"},{"first_name":"Reinhard","last_name":"Lipowsky","full_name":"Lipowsky, Reinhard"}],"doi":"10.1021/acs.nanolett.9b04445","_id":"7166","publisher":"American Chemical Society","main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.9b04445","open_access":"1"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9726"},{"id":"9885","status":"public","relation":"research_data"}]},"abstract":[{"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.","lang":"eng"}],"article_type":"letter_note","publication_status":"published","date_published":"2020-01-08T00:00:00Z","volume":20,"oa":1,"year":"2020","month":"01","oa_version":"Published Version","external_id":{"pmid":["31797672"],"isi":["000507151600087"]},"day":"08","article_processing_charge":"No","title":"Collective force generation by molecular motors is determined by strain-induced unbinding","date_updated":"2026-07-06T12:14:33Z","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","page":"669-676","citation":{"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","short":"M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676.","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.","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."},"publication":"Nano Letters","isi":1,"scopus_import":"1","status":"public","department":[{"_id":"EdHa"}],"pmid":1,"ddc":["570"],"corr_author":"1","issue":"1"},{"language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","date_updated":"2026-07-06T12:43:42Z","title":"Gene regulation across scales – how biophysical constraints shape evolution","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"ddc":["530","570"],"corr_author":"1","degree_awarded":"PhD","citation":{"ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","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","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","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.","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."},"page":"310","status":"public","publisher":"Institute of Science and Technology Austria","_id":"8155","supervisor":[{"first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"file":[{"date_updated":"2020-07-27T12:00:07Z","date_created":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","creator":"rgrah","content_type":"application/pdf","file_size":16638998,"access_level":"open_access","relation":"main_file","success":1,"file_id":"8176"},{"file_name":"Thesis_new.zip","date_created":"2020-07-27T12:02:23Z","creator":"rgrah","date_updated":"2020-07-30T13:04:55Z","access_level":"closed","file_size":347459978,"content_type":"application/zip","file_id":"8177","relation":"main_file"}],"type":"dissertation","project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:8155","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","first_name":"Rok","last_name":"Grah"}],"date_created":"2020-07-23T09:51:28Z","month":"07","has_accepted_license":"1","OA_place":"publisher","day":"24","oa_version":"Published Version","publication_status":"published","abstract":[{"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. ","lang":"eng"}],"file_date_updated":"2020-07-30T13:04:55Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"7569","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7652"},{"id":"7675","status":"public","relation":"part_of_dissertation"}]},"oa":1,"year":"2020","date_published":"2020-07-24T00:00:00Z","alternative_title":["ISTA Thesis"]},{"oa":1,"year":"2020","status":"public","date_published":"2020-04-09T00:00:00Z","das_tickbox":"1","publication_status":"published","biorxivid":1,"abstract":[{"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.","lang":"eng"}],"publication":"bioRxiv","citation":{"apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. https://doi.org/10.1101/2020.04.08.029405","ama":"Grah R, Zoller B, Tkačik G. 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.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv, 2020. https://doi.org/10.1101/2020.04.08.029405.","mla":"Grah, Rok, et al. “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."},"related_material":{"record":[{"status":"public","id":"8155","relation":"dissertation_contains"}]},"corr_author":"1","day":"09","external_id":{"biorxivid":["10.1101/2020.04.08.029405"]},"oa_version":"Preprint","month":"04","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"project":[{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","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"}],"doi":"10.1101/2020.04.08.029405","date_updated":"2026-07-06T12:43:43Z","date_created":"2020-04-23T10:12:51Z","title":"Normative models of enhancer function","author":[{"first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"Benjamin","last_name":"Zoller","full_name":"Zoller, Benjamin"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"type":"preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2020.04.08.029405 ","open_access":"1"}],"_id":"7675"},{"oa":1,"year":"2020","status":"public","date_published":"2020-11-05T00:00:00Z","das_tickbox":"1","publication_status":"submitted","abstract":[{"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.","lang":"eng"}],"publication":"bioRxiv","citation":{"ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. .","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","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","mla":"Santini, Laura, 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.","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.","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.)."},"day":"05","external_id":{"pmid":["PPR234457 "]},"oa_version":"Preprint","month":"11","pmid":1,"department":[{"_id":"SiHi"}],"doi":"10.1101/2020.11.03.366948","date_updated":"2026-07-06T12:45:07Z","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","date_created":"2020-11-26T07:17:19Z","author":[{"last_name":"Santini","first_name":"Laura","full_name":"Santini, Laura"},{"last_name":"Halbritter","first_name":"Florian","full_name":"Halbritter, Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"first_name":"Toru","last_name":"Suzuki","full_name":"Suzuki, Toru"},{"last_name":"Asami","first_name":"Maki","full_name":"Asami, Maki"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"full_name":"Ma, Xiaoyan","first_name":"Xiaoyan","last_name":"Ma"},{"last_name":"Lackner","first_name":"Andreas","full_name":"Lackner, Andreas"},{"full_name":"Warr, Nick","first_name":"Nick","last_name":"Warr"},{"first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Laue, Ernest","last_name":"Laue","first_name":"Ernest"},{"full_name":"Farlik, Matthias","last_name":"Farlik","first_name":"Matthias"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F.","last_name":"Perry"},{"last_name":"Leeb","first_name":"Martin","full_name":"Leeb, Martin"}],"type":"preprint","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"_id":"8813"},{"date_published":"2020-02-19T00:00:00Z","status":"public","oa":1,"year":"2020","das_tickbox":"1","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."}],"publication_status":"published","page":"22","citation":{"short":"Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020).","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.","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.","mla":"Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” BioRxiv, 2020, doi:10.1101/791137.","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","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","ieee":"Z. Wei et al., “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” bioRxiv. 2020."},"publication":"bioRxiv","day":"19","oa_version":"Preprint","month":"02","department":[{"_id":"JiFr"}],"date_updated":"2026-07-06T12:53:37Z","doi":"10.1101/791137","date_created":"2020-03-21T16:34:42Z","author":[{"last_name":"Wei","first_name":"Zhuang","full_name":"Wei, Zhuang"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"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","first_name":"Ji-Gang","last_name":"Lei"},{"last_name":"Chen","first_name":"ZhengJun","full_name":"Chen, ZhengJun"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"},{"first_name":"Kan","last_name":"Liao","full_name":"Liao, Kan"}],"title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","type":"preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"_id":"7601"},{"issue":"3","department":[{"_id":"TaHa"}],"status":"public","das_tickbox":"1","isi":1,"scopus_import":"1","citation":{"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.","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.","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.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 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."},"page":"663-671","publication":"Annales Scientifiques de l'Ecole Normale Superieure","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2026-07-06T13:57:35Z","publication_identifier":{"issn":["0012-9593"]},"title":"On the K-theory stable bases of the springer resolution","article_processing_charge":"No","day":"01","oa_version":"Preprint","external_id":{"arxiv":["1708.08013"],"isi":["000592182600004"]},"month":"06","volume":53,"date_published":"2020-06-01T00:00:00Z","oa":1,"year":"2020","arxiv":1,"abstract":[{"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.","lang":"eng"},{"lang":"fre","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. "}],"article_type":"original","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08013"}],"publisher":"Societe Mathematique de France","_id":"8539","doi":"10.24033/asens.2431","author":[{"full_name":"Su, C.","last_name":"Su","first_name":"C."},{"id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","full_name":"Zhao, Gufang","orcid":"0000-0001-7361-2882","first_name":"Gufang","last_name":"Zhao"},{"last_name":"Zhong","first_name":"C.","full_name":"Zhong, C."}],"date_created":"2020-09-20T22:01:38Z","type":"journal_article","intvolume":" 53"},{"date_updated":"2026-07-06T14:02:25Z","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.","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"das_tickbox":"1","isi":1,"scopus_import":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"page":"605-622","citation":{"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.","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.","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.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 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.","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","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"},"publication":"SIAM Journal on Mathematical Analysis","ddc":["510"],"corr_author":"1","issue":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"RoSe"}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"doi":"10.1137/19m126284x","date_created":"2021-08-06T07:34:16Z","author":[{"first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"type":"journal_article","intvolume":" 52","publisher":"Society for Industrial and Applied Mathematics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.08647"}],"_id":"9781","volume":52,"date_published":"2020-02-12T00:00:00Z","year":"2020","oa":1,"arxiv":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"}],"publication_status":"published","article_type":"original","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"}]},"day":"12","oa_version":"Preprint","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"ec_funded":1,"has_accepted_license":"1","month":"02"},{"alternative_title":["ISTA Thesis"],"date_published":"2020-12-21T00:00:00Z","year":"2020","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8587"},{"relation":"part_of_dissertation","id":"1120","status":"public"},{"relation":"part_of_dissertation","id":"5886","status":"public"}]},"file_date_updated":"2020-12-30T07:18:03Z","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."}],"publication_status":"published","oa_version":"Published Version","ec_funded":1,"day":"21","OA_place":"publisher","has_accepted_license":"1","month":"12","author":[{"first_name":"Xiang","last_name":"Li","full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-12-21T09:44:30Z","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770"}],"doi":"10.15479/AT:ISTA:8958","type":"dissertation","file":[{"creator":"xli","file_name":"THESIS_Xiang_Li.pdf","date_created":"2020-12-22T10:55:56Z","date_updated":"2020-12-22T10:55:56Z","file_id":"8967","relation":"main_file","checksum":"3994c54a1241451d561db1d4f43bad30","success":1,"file_size":3622305,"access_level":"open_access","content_type":"application/pdf"},{"content_type":"application/x-zip-compressed","file_size":4018859,"access_level":"closed","checksum":"0954ecfc5554c05615c14de803341f00","relation":"source_file","file_id":"8968","date_updated":"2020-12-30T07:18:03Z","date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip","creator":"xli"}],"_id":"8958","supervisor":[{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail"}],"publisher":"Institute of Science and Technology Austria","status":"public","page":"125","citation":{"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.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","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.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","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","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."},"degree_awarded":"PhD","corr_author":"1","ddc":["539"],"department":[{"_id":"MiLe"}],"title":"Rotation of coupled cold molecules in the presence of a many-body environment","date_updated":"2026-07-07T05:31:09Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}]},{"type":"conference","intvolume":" 179","author":[{"first_name":"Sebastian","last_name":"Brandt","full_name":"Brandt, Sebastian"},{"full_name":"Keller, Barbara","first_name":"Barbara","last_name":"Keller"},{"first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"},{"full_name":"Suomela, Jukka","first_name":"Jukka","last_name":"Suomela"},{"last_name":"Uitto","first_name":"Jara","full_name":"Uitto, Jara"}],"date_created":"2024-03-05T07:09:12Z","doi":"10.4230/LIPIcs.DISC.2020.40","_id":"15074","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"file_id":"15075","relation":"main_file","success":1,"checksum":"23e2d9321aef53092dc1e24a8ab82d72","access_level":"open_access","file_size":303529,"content_type":"application/pdf","date_created":"2024-03-05T07:08:27Z","file_name":"2020_LIPIcs_Brandt.pdf","creator":"dernst","date_updated":"2024-03-05T07:08:27Z"}],"file_date_updated":"2024-03-05T07:08:27Z","related_material":{"record":[{"id":"9678","status":"public","relation":"later_version"}]},"publication_status":"published","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."}],"arxiv":1,"alternative_title":["LIPIcs"],"year":"2020","oa":1,"date_published":"2020-10-07T00:00:00Z","volume":179,"month":"10","has_accepted_license":"1","external_id":{"arxiv":["2005.07761"]},"oa_version":"Published Version","day":"07","article_processing_charge":"No","article_number":"40","title":"Brief announcement: Efficient load-balancing through distributed token dropping","date_updated":"2026-07-07T06:21:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"start_date":"2020-10-12","location":"Virtual","end_date":"2020-10-16","name":"DISC: Symposium on Distributed Computing"},"quality_controlled":"1","publication":"34th International Symposium on Distributed Computing","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)"},"citation":{"short":"S. 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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. 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Alistarh, in:, 37th International Conference on Machine Learning, 2020, pp. 5533–5543.","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.","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.","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."},"page":"5533-5543","publication":"37th International Conference on Machine Learning","status":"public","das_tickbox":"1","department":[{"_id":"DaAl"}],"ddc":["000"],"article_processing_charge":"No","date_updated":"2026-07-07T13:42:32Z","publication_identifier":{"issn":["2640-3498"]},"title":"Inducing and exploiting activation sparsity for fast neural network inference","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"start_date":"2020-07-12","location":"Online","end_date":"2020-07-18","name":"ICML: International Conference on Machine Learning"}},{"doi":"10.1103/PhysRevLett.125.043202","date_created":"2020-08-24T06:24:04Z","author":[{"last_name":"Malia","first_name":"Benjamin K.","full_name":"Malia, Benjamin K."},{"first_name":"Julián","last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián"},{"last_name":"Wu","first_name":"Yunfan","full_name":"Wu, Yunfan"},{"last_name":"Hosten","first_name":"Onur","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kasevich, Mark A.","last_name":"Kasevich","first_name":"Mark A."}],"type":"journal_article","intvolume":" 125","publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/1912.10218","open_access":"1"}],"_id":"8285","year":"2020","oa":1,"volume":125,"date_published":"2020-07-24T00:00:00Z","arxiv":1,"article_type":"original","publication_status":"published","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."}],"researchdata_availability":"no","day":"24","external_id":{"pmid":["32794788"],"isi":["000552227400008"],"arxiv":["1912.10218"]},"oa_version":"Preprint","month":"07","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"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).","date_updated":"2026-07-08T08:56:44Z","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","article_number":"043202","article_processing_charge":"No","quality_controlled":"1","supplementarymaterial":"yes","language":[{"iso":"eng"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","status":"public","das_tickbox":"0","scopus_import":"1","isi":1,"publication":"Physical Review Letters","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.","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","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","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.","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. 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In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.","lang":"eng"}],"year":"2020","oa":1,"volume":102,"date_published":"2020-07-30T00:00:00Z","arxiv":1,"quality_controlled":"1","supplementarymaterial":"no","language":[{"iso":"eng"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_number":"012224","article_processing_charge":"No","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","date_updated":"2026-07-08T08:59:02Z","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","department":[{"_id":"OnHo"}],"issue":"1","scopus_import":"1","isi":1,"publication":"Physical Review A","citation":{"short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. 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Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.","lang":"eng"}],"file":[{"access_level":"open_access","file_size":17355867,"content_type":"application/pdf","file_id":"8709","success":1,"relation":"main_file","checksum":"c4300ddcd93ed03fc9c6cdf1f77890be","date_created":"2020-10-27T11:37:32Z","file_name":"2020_eLife_Gonçalves.pdf","creator":"cziletti","date_updated":"2020-10-27T11:37:32Z"}],"_id":"8127","publisher":"eLife Sciences Publications","date_created":"2020-07-16T12:26:04Z","author":[{"orcid":"0000-0002-6987-4836","full_name":"Gonçalves, Pedro J.","last_name":"Gonçalves","first_name":"Pedro J."},{"full_name":"Lueckmann, Jan-Matthis","orcid":"0000-0003-4320-4663","first_name":"Jan-Matthis","last_name":"Lueckmann"},{"last_name":"Deistler","first_name":"Michael","orcid":"0000-0002-3573-0404","full_name":"Deistler, Michael"},{"orcid":"0000-0001-6044-6627","full_name":"Nonnenmacher, Marcel","last_name":"Nonnenmacher","first_name":"Marcel"},{"orcid":"0000-0002-8528-6858","full_name":"Öcal, Kaan","last_name":"Öcal","first_name":"Kaan"},{"full_name":"Bassetto, Giacomo","first_name":"Giacomo","last_name":"Bassetto"},{"id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","full_name":"Chintaluri, Chaitanya","orcid":"0000-0003-4252-1608","first_name":"Chaitanya","last_name":"Chintaluri"},{"orcid":"0000-0001-6619-7502","full_name":"Podlaski, William F.","last_name":"Podlaski","first_name":"William F."},{"last_name":"Haddad","first_name":"Sara A.","orcid":"0000-0003-0807-0823","full_name":"Haddad, Sara A."},{"orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"},{"first_name":"David S.","last_name":"Greenberg","full_name":"Greenberg, David S."},{"first_name":"Jakob H.","last_name":"Macke","full_name":"Macke, Jakob H.","orcid":"0000-0001-5154-8912"}],"project":[{"grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"doi":"10.7554/eLife.56261","intvolume":" 9","type":"journal_article","ddc":["570"],"pmid":1,"department":[{"_id":"TiVo"}],"das_tickbox":"1","status":"public","publication":"eLife","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.56261","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 2020;9. doi:10.7554/eLife.56261","ieee":"P. J. Gonçalves et al., “Training deep neural density estimators to identify mechanistic models of neural dynamics,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.56261.","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” ELife, vol. 9, e56261, eLife Sciences Publications, 2020, doi:10.7554/eLife.56261.","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261."},"scopus_import":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","publication_identifier":{"eissn":["2050-084X"]},"acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","date_updated":"2026-07-13T12:31:21Z","article_processing_charge":"No","article_number":"e56261"},{"publication_identifier":{"issn":["1042-9832"],"eissn":["1098-2418"]},"date_updated":"2026-07-14T08:31:05Z","title":"Ramsey, Paper, Scissors","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"OA_type":"green","status":"public","scopus_import":"1","publication":"Random Structures & Algorithms","citation":{"mla":"Fox, Jacob, et al. “Ramsey, Paper, Scissors.” Random Structures & Algorithms, vol. 57, no. 4, Wiley, 2020, pp. 1157–73, doi:10.1002/rsa.20950.","ista":"Fox J, He X, Wigderson Y. 2020. Ramsey, Paper, Scissors. Random Structures & Algorithms. 57(4), 1157–1173.","chicago":"Fox, Jacob, Xiaoyu He, and Yuval Wigderson. “Ramsey, Paper, Scissors.” Random Structures & Algorithms. Wiley, 2020. https://doi.org/10.1002/rsa.20950.","short":"J. Fox, X. He, Y. Wigderson, Random Structures & Algorithms 57 (2020) 1157–1173.","ieee":"J. Fox, X. He, and Y. Wigderson, “Ramsey, Paper, Scissors,” Random Structures & Algorithms, vol. 57, no. 4. Wiley, pp. 1157–1173, 2020.","apa":"Fox, J., He, X., & Wigderson, Y. (2020). Ramsey, Paper, Scissors. Random Structures & Algorithms. Wiley. https://doi.org/10.1002/rsa.20950","ama":"Fox J, He X, Wigderson Y. Ramsey, Paper, Scissors. Random Structures & Algorithms. 2020;57(4):1157-1173. doi:10.1002/rsa.20950"},"page":"1157-1173","issue":"4","doi":"10.1002/rsa.20950","author":[{"first_name":"Jacob","last_name":"Fox","full_name":"Fox, Jacob"},{"full_name":"He, Xiaoyu","first_name":"Xiaoyu","last_name":"He"},{"last_name":"Wigderson","first_name":"Yuval","full_name":"Wigderson, Yuval","id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5"}],"date_created":"2026-06-29T10:54:10Z","type":"journal_article","intvolume":" 57","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1906.01092"}],"_id":"22166","year":"2020","oa":1,"date_published":"2020-12-01T00:00:00Z","volume":57,"arxiv":1,"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"We introduce a graph Ramsey game called Ramsey, Paper,Scissors. This game has two players, Proposer and Decider.Starting from an empty graph on n vertices, on each turnProposer proposes a potential edge and Decider simultane-ously decides (without knowing Proposer’s choice) whether toadd it to the graph. Proposer cannot propose an edge whichwould create a triangle in the graph. The game ends whenProposer has no legal moves remaining, and Proposer wins ifthe final graph has independence number at least s. We provea threshold phenomenon exists for this game by exhibitingrandomized strategies for both players that are optimal up toconstants. Namely, there exist constants 0 < A < B such that(under optimal play) Proposer wins with high probability ifs < A√n log n, while Decider wins with high probability ifs > B√n log n. This is a factor of Θ(√log n)) larger than thelower bound coming from the off-diagonal Ramsey numberr(3, s)."}],"OA_place":"repository","day":"01","external_id":{"arxiv":["1906.01092"]},"oa_version":"Preprint","extern":"1","month":"12"},{"status":"public","scopus_import":"1","publication":"Comptes Rendus Mathématique","page":"957-959","citation":{"ieee":"J. Fox, Y. Wigderson, and Y. Zhao, “A short proof of the canonical polynomial van der Waerden theorem,” Comptes Rendus Mathématique, vol. 358, no. 8. Académie des Sciences, pp. 957–959, 2020.","apa":"Fox, J., Wigderson, Y., & Zhao, Y. (2020). A short proof of the canonical polynomial van der Waerden theorem. Comptes Rendus Mathématique. Académie des Sciences. https://doi.org/10.5802/crmath.101","ama":"Fox J, Wigderson Y, Zhao Y. A short proof of the canonical polynomial van der Waerden theorem. Comptes Rendus Mathématique. 2020;358(8):957-959. doi:10.5802/crmath.101","ista":"Fox J, Wigderson Y, Zhao Y. 2020. A short proof of the canonical polynomial van der Waerden theorem. Comptes Rendus Mathématique. 358(8), 957–959.","mla":"Fox, Jacob, et al. “A Short Proof of the Canonical Polynomial van Der Waerden Theorem.” Comptes Rendus Mathématique, vol. 358, no. 8, Académie des Sciences, 2020, pp. 957–59, doi:10.5802/crmath.101.","chicago":"Fox, Jacob, Yuval Wigderson, and Yufei Zhao. “A Short Proof of the Canonical Polynomial van Der Waerden Theorem.” Comptes Rendus Mathématique. Académie des Sciences, 2020. https://doi.org/10.5802/crmath.101.","short":"J. Fox, Y. Wigderson, Y. Zhao, Comptes Rendus Mathématique 358 (2020) 957–959."},"issue":"8","publication_identifier":{"eissn":["1778-3569"],"issn":["1631-073X"]},"date_updated":"2026-07-14T09:19:20Z","title":"A short proof of the canonical polynomial van der Waerden theorem","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","year":"2020","oa":1,"date_published":"2020-12-03T00:00:00Z","volume":358,"arxiv":1,"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"We present a short new proof of the canonical polynomial van der Waerden theorem, recently established by Girão."}],"OA_place":"repository","day":"03","external_id":{"arxiv":["2005.04135"]},"oa_version":"Preprint","extern":"1","month":"12","doi":"10.5802/crmath.101","author":[{"full_name":"Fox, Jacob","last_name":"Fox","first_name":"Jacob"},{"full_name":"Wigderson, Yuval","id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5","last_name":"Wigderson","first_name":"Yuval"},{"full_name":"Zhao, Yufei","last_name":"Zhao","first_name":"Yufei"}],"date_created":"2026-06-29T11:00:09Z","type":"journal_article","intvolume":" 358","publisher":"Académie des Sciences","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2005.04135","open_access":"1"}],"_id":"22182","mathsc":["05D10","11B30"]},{"external_id":{"arxiv":["1910.06287"]},"oa_version":"Preprint","OA_place":"repository","day":"01","month":"02","extern":"1","arxiv":1,"year":"2020","oa":1,"date_published":"2020-02-01T00:00:00Z","volume":27,"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"A weakly optimal Ks-free (n,d,λ)-graph is ad-regular Ks-free graph on n vertices with d= Θ(n1−α) and spectral expansion λ= Θ(n1−(s−1)α), for some fixed α >0. Such a graph is called optimal if additionally α=12s−3. We prove that if s1,...,sk>3 are fixed positive integers and weakly optimal Ksi-free pseudorandom graphs exist for each 1The Electronic Journal of Combinatorics, vol. 27, no. 1. The Electronic Journal of Combinatorics, 2020.","ama":"He X, Wigderson Y. Multicolor Ramsey numbers via pseudorandom graphs. The Electronic Journal of Combinatorics. 2020;27(1). doi:10.37236/9071","apa":"He, X., & Wigderson, Y. (2020). Multicolor Ramsey numbers via pseudorandom graphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/9071","short":"X. He, Y. Wigderson, The Electronic Journal of Combinatorics 27 (2020).","mla":"He, Xiaoyu, and Yuval Wigderson. “Multicolor Ramsey Numbers via Pseudorandom Graphs.” The Electronic Journal of Combinatorics, vol. 27, no. 1, P1.32, The Electronic Journal of Combinatorics, 2020, doi:10.37236/9071.","ista":"He X, Wigderson Y. 2020. Multicolor Ramsey numbers via pseudorandom graphs. The Electronic Journal of Combinatorics. 27(1), P1.32.","chicago":"He, Xiaoyu, and Yuval Wigderson. “Multicolor Ramsey Numbers via Pseudorandom Graphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2020. https://doi.org/10.37236/9071."},"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","OA_type":"green","title":"Multicolor Ramsey numbers via pseudorandom graphs","publication_identifier":{"eissn":["1077-8926"]},"date_updated":"2026-07-14T09:42:53Z","article_processing_charge":"No","article_number":"P1.32"}]