--- OA_place: repository OA_type: green _id: '22080' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yannis full_name: Angelopoulos, Yannis last_name: Angelopoulos - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: 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 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 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. 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. 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. short: Y. Angelopoulos, R. Killip, M. Vişan, SIAM Journal on Mathematical Analysis 52 (2020) 135–163. das_tickbox: '1' date_created: 2026-06-19T08:26:32Z date_published: 2020-01-01T00:00:00Z date_updated: 2026-06-30T12:21:20Z day: '01' doi: 10.1137/19m1265314 extern: '1' external_id: arxiv: - '1807.08801' intvolume: ' 52' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1807.08801 mathsc: - 35Q55 - 35Q51 - 35Q82 month: '01' oa: 1 oa_version: Preprint page: 135-163 publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - 1095-7154 issn: - 0036-1410 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Invariant measures for integrable spin chains and an integrable discrete nonlinear Schrödinger equation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2020' ... --- _id: '8042' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Chiara full_name: Boccato, Chiara id: 342E7E22-F248-11E8-B48F-1D18A9856A87 last_name: Boccato - first_name: Christian full_name: Brennecke, Christian last_name: Brennecke - first_name: Serena full_name: Cenatiempo, Serena last_name: Cenatiempo - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein citation: 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 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 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. 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. 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. short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European Mathematical Society 22 (2020) 2331–2403. das_tickbox: '1' date_created: 2020-06-29T07:59:35Z date_published: 2020-07-01T00:00:00Z date_updated: 2026-07-06T11:53:41Z day: '01' department: - _id: RoSe doi: 10.4171/JEMS/966 external_id: arxiv: - '1704.04819' isi: - '000548174700006' intvolume: ' 22' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.04819 month: '07' oa: 1 oa_version: Preprint page: 2331-2403 publication: Journal of the European Mathematical Society publication_identifier: issn: - 1435-9855 publication_status: published publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: The excitation spectrum of Bose gases interacting through singular potentials type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2020' ... --- _id: '9007' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Will full_name: Sawin, Will last_name: Sawin 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 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 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. 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. 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. short: T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659. das_tickbox: '1' date_created: 2021-01-17T23:01:11Z date_published: 2020-12-07T00:00:00Z date_updated: 2026-07-06T11:54:01Z day: '07' department: - _id: TiBr doi: 10.4171/CMH/499 external_id: arxiv: - '1906.08463' isi: - '000596833300001' intvolume: ' 95' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.08463 month: '12' oa: 1 oa_version: Preprint page: 635-659 publication: Commentarii Mathematici Helvetici publication_identifier: eissn: - 1420-8946 issn: - 0010-2571 publication_status: published publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: Free rational points on smooth hypersurfaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2020' ... --- _id: '8973' 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. 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_number: '138' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Frank full_name: Redig, Frank last_name: Redig - first_name: Ellen full_name: Saada, Ellen last_name: Saada - first_name: Federico full_name: Sau, Federico id: E1836206-9F16-11E9-8814-AEFDE5697425 last_name: Sau citation: 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' 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.' 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.' ista: 'Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.' mla: 'Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.' short: F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020). das_tickbox: '1' date_created: 2020-12-27T23:01:17Z date_published: 2020-10-21T00:00:00Z date_updated: 2026-07-06T12:04:40Z day: '21' ddc: - '510' department: - _id: JaMa doi: 10.1214/20-EJP536 ec_funded: 1 external_id: arxiv: - '1811.01366' isi: - '000591737500001' file: - access_level: open_access checksum: d75359b9814e78d57c0a481b7cde3751 content_type: application/pdf creator: dernst date_created: 2020-12-28T08:24:08Z date_updated: 2020-12-28T08:24:08Z file_id: '8976' file_name: 2020_ElectronJProbab_Redig.pdf file_size: 696653 relation: main_file success: 1 file_date_updated: 2020-12-28T08:24:08Z has_accepted_license: '1' intvolume: ' 25' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Electronic Journal of Probability publication_identifier: eissn: - 1083-6489 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: 'Symmetric simple exclusion process in dynamic environment: Hydrodynamics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2020' ... --- _id: '7166' 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. article_processing_charge: No article_type: letter_note author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Reinhard full_name: Lipowsky, Reinhard last_name: Lipowsky citation: 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 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. 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. ista: Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 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. short: M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676. corr_author: '1' date_created: 2019-12-10T15:36:05Z date_published: 2020-01-08T00:00:00Z date_updated: 2026-07-06T12:14:33Z day: '08' ddc: - '570' department: - _id: EdHa doi: 10.1021/acs.nanolett.9b04445 external_id: isi: - '000507151600087' pmid: - '31797672' intvolume: ' 20' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acs.nanolett.9b04445 month: '01' oa: 1 oa_version: Published Version page: 669-676 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '9726' relation: research_data status: public - id: '9885' relation: research_data status: public scopus_import: '1' status: public title: Collective force generation by molecular motors is determined by strain-induced unbinding type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2020' ... --- OA_place: publisher _id: '8155' 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. " acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 citation: 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 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. ieee: 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. short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-07-23T09:51:28Z date_published: 2020-07-24T00:00:00Z date_updated: 2026-07-06T12:43:42Z day: '24' ddc: - '530' - '570' degree_awarded: PhD department: - _id: CaGu - _id: GaTk doi: 10.15479/AT:ISTA:8155 file: - access_level: open_access content_type: application/pdf creator: rgrah date_created: 2020-07-27T12:00:07Z date_updated: 2020-07-27T12:00:07Z file_id: '8176' file_name: Thesis_RokGrah_200727_convertedNew.pdf file_size: 16638998 relation: main_file success: 1 - access_level: closed content_type: application/zip creator: rgrah date_created: 2020-07-27T12:02:23Z date_updated: 2020-07-30T13:04:55Z file_id: '8177' file_name: Thesis_new.zip file_size: 347459978 relation: main_file file_date_updated: 2020-07-30T13:04:55Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '310' project: - _id: 267C84F4-B435-11E9-9278-68D0E5697425 name: Biophysically realistic genotype-phenotype maps for regulatory networks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7569' relation: part_of_dissertation status: public - id: '7652' relation: part_of_dissertation status: public - id: '7675' relation: part_of_dissertation status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Gene regulation across scales – how biophysical constraints shape evolution type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- _id: '7675' 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.' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Benjamin full_name: Zoller, Benjamin last_name: Zoller - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 biorxivid: 1 citation: ama: Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi: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. ieee: R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. 2020. ista: Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 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. short: R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020). corr_author: '1' das_tickbox: '1' date_created: 2020-04-23T10:12:51Z date_published: 2020-04-09T00:00:00Z date_updated: 2026-07-06T12:43:43Z day: '09' department: - _id: CaGu - _id: GaTk doi: 10.1101/2020.04.08.029405 external_id: biorxivid: - 10.1101/2020.04.08.029405 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/2020.04.08.029405 ' month: '04' oa: 1 oa_version: Preprint 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 publication: bioRxiv publication_status: published related_material: record: - id: '8155' relation: dissertation_contains status: public status: public title: Normative models of enhancer function type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8813' 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.' article_processing_charge: No author: - first_name: Laura full_name: Santini, Laura last_name: Santini - first_name: Florian full_name: Halbritter, Florian last_name: Halbritter - first_name: Fabian full_name: Titz-Teixeira, Fabian last_name: Titz-Teixeira - first_name: Toru full_name: Suzuki, Toru last_name: Suzuki - first_name: Maki full_name: Asami, Maki last_name: Asami - first_name: Julia full_name: Ramesmayer, Julia last_name: Ramesmayer - first_name: Xiaoyan full_name: Ma, Xiaoyan last_name: Ma - first_name: Andreas full_name: Lackner, Andreas last_name: Lackner - first_name: Nick full_name: Warr, Nick last_name: Warr - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ernest full_name: Laue, Ernest last_name: Laue - first_name: Matthias full_name: Farlik, Matthias last_name: Farlik - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Andreas full_name: Beyer, Andreas last_name: Beyer - first_name: Anthony C. F. full_name: Perry, Anthony C. F. last_name: Perry - first_name: Martin full_name: Leeb, Martin last_name: Leeb citation: 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 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. ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. . 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. 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.). das_tickbox: '1' date_created: 2020-11-26T07:17:19Z date_published: 2020-11-05T00:00:00Z date_updated: 2026-07-06T12:45:07Z day: '05' department: - _id: SiHi doi: 10.1101/2020.11.03.366948 external_id: pmid: - 'PPR234457 ' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.11.03.366948 month: '11' oa: 1 oa_version: Preprint pmid: 1 publication: bioRxiv publication_status: submitted status: public title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7601' 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. article_processing_charge: No author: - first_name: Zhuang full_name: Wei, Zhuang last_name: Wei - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Tao full_name: Liu, Tao last_name: Liu - first_name: Yuan full_name: Wu, Yuan last_name: Wu - first_name: Ji-Gang full_name: Lei, Ji-Gang last_name: Lei - first_name: ZhengJun full_name: Chen, ZhengJun last_name: Chen - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Hong-Wei full_name: Xue, Hong-Wei last_name: Xue - first_name: Kan full_name: Liao, Kan last_name: Liao citation: 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 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. ieee: Z. Wei et al., “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” bioRxiv. 2020. 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. short: Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020). das_tickbox: '1' date_created: 2020-03-21T16:34:42Z date_published: 2020-02-19T00:00:00Z date_updated: 2026-07-06T12:53:37Z day: '19' department: - _id: JiFr doi: 10.1101/791137 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/791137 month: '02' oa: 1 oa_version: Preprint page: '22' publication: bioRxiv publication_status: published status: public title: Plasmodesmata-like intercellular connections by plant remorin in animal cells type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8539' 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. - 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_processing_charge: No article_type: original arxiv: 1 author: - first_name: C. full_name: Su, C. last_name: Su - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao orcid: 0000-0001-7361-2882 - first_name: C. full_name: Zhong, C. last_name: Zhong citation: 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 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. 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. 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. 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. das_tickbox: '1' date_created: 2020-09-20T22:01:38Z date_published: 2020-06-01T00:00:00Z date_updated: 2026-07-06T13:57:35Z day: '01' department: - _id: TaHa doi: 10.24033/asens.2431 external_id: arxiv: - '1708.08013' isi: - '000592182600004' intvolume: ' 53' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.08013 month: '06' oa: 1 oa_version: Preprint page: 663-671 publication: Annales Scientifiques de l'Ecole Normale Superieure publication_identifier: issn: - 0012-9593 publication_status: published publisher: Societe Mathematique de France quality_controlled: '1' scopus_import: '1' status: public title: On the K-theory stable bases of the springer resolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2020' ... --- _id: '9781' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 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 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. 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. 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. 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. corr_author: '1' das_tickbox: '1' date_created: 2021-08-06T07:34:16Z date_published: 2020-02-12T00:00:00Z date_updated: 2026-07-06T14:02:25Z day: '12' ddc: - '510' department: - _id: RoSe doi: 10.1137/19m126284x ec_funded: 1 external_id: arxiv: - '1904.08647 ' isi: - '000546967700022' has_accepted_license: '1' intvolume: ' 52' isi: 1 issue: '1' keyword: - Applied Mathematics - Computational Mathematics - Analysis language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.08647 month: '02' oa: 1 oa_version: Preprint page: 605-622 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - 1095-7154 issn: - 0036-1410 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '9733' relation: dissertation_contains status: public scopus_import: '1' status: public title: Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2020' ... --- OA_place: publisher _id: '8958' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi: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 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. ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020. 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. corr_author: '1' date_created: 2020-12-21T09:44:30Z date_published: 2020-12-21T00:00:00Z date_updated: 2026-07-07T05:31:09Z day: '21' ddc: - '539' degree_awarded: PhD department: - _id: MiLe doi: 10.15479/AT:ISTA:8958 ec_funded: 1 file: - access_level: open_access checksum: 3994c54a1241451d561db1d4f43bad30 content_type: application/pdf creator: xli date_created: 2020-12-22T10:55:56Z date_updated: 2020-12-22T10:55:56Z file_id: '8967' file_name: THESIS_Xiang_Li.pdf file_size: 3622305 relation: main_file success: 1 - access_level: closed checksum: 0954ecfc5554c05615c14de803341f00 content_type: application/x-zip-compressed creator: xli date_created: 2020-12-22T10:56:03Z date_updated: 2020-12-30T07:18:03Z file_id: '8968' file_name: THESIS_Xiang_Li.zip file_size: 4018859 relation: source_file file_date_updated: 2020-12-30T07:18:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '125' project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8587' relation: part_of_dissertation status: public - id: '1120' relation: part_of_dissertation status: public - id: '5886' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Rotation of coupled cold molecules in the presence of a many-body environment type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- _id: '15074' 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. alternative_title: - LIPIcs article_number: '40' article_processing_charge: No arxiv: 1 author: - first_name: Sebastian full_name: Brandt, Sebastian last_name: Brandt - first_name: Barbara full_name: Keller, Barbara last_name: Keller - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Jukka full_name: Suomela, Jukka last_name: Suomela - first_name: Jara full_name: Uitto, Jara last_name: Uitto citation: 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' 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' 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.' 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.' 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.' 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.' 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. conference: end_date: 2020-10-16 location: Virtual name: 'DISC: Symposium on Distributed Computing' start_date: 2020-10-12 corr_author: '1' date_created: 2024-03-05T07:09:12Z date_published: 2020-10-07T00:00:00Z date_updated: 2026-07-07T06:21:32Z day: '07' ddc: - '000' department: - _id: DaAl doi: 10.4230/LIPIcs.DISC.2020.40 external_id: arxiv: - '2005.07761' file: - access_level: open_access checksum: 23e2d9321aef53092dc1e24a8ab82d72 content_type: application/pdf creator: dernst date_created: 2024-03-05T07:08:27Z date_updated: 2024-03-05T07:08:27Z file_id: '15075' file_name: 2020_LIPIcs_Brandt.pdf file_size: 303529 relation: main_file success: 1 file_date_updated: 2024-03-05T07:08:27Z has_accepted_license: '1' intvolume: ' 179' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '10' oa: 1 oa_version: Published Version publication: 34th International Symposium on Distributed Computing publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '9678' relation: later_version status: public scopus_import: '1' status: public title: 'Brief announcement: Efficient load-balancing through distributed token dropping' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 179 year: '2020' ... --- _id: '9415' 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. ' article_processing_charge: No author: - first_name: Mark full_name: Kurtz, Mark last_name: Kurtz - first_name: Justin full_name: Kopinsky, Justin last_name: Kopinsky - first_name: Rati full_name: Gelashvili, Rati last_name: Gelashvili - first_name: Alexander full_name: Matveev, Alexander last_name: Matveev - first_name: John full_name: Carr, John last_name: Carr - first_name: Michael full_name: Goin, Michael last_name: Goin - first_name: William full_name: Leiserson, William last_name: Leiserson - first_name: Sage full_name: Moore, Sage last_name: Moore - first_name: Bill full_name: Nell, Bill last_name: Nell - first_name: Nir full_name: Shavit, Nir last_name: Shavit - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: 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.' 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. 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. 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.' 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. 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. conference: end_date: 2020-07-18 location: Online name: 'ICML: International Conference on Machine Learning' start_date: 2020-07-12 das_tickbox: '1' date_created: 2021-05-23T22:01:45Z date_published: 2020-07-12T00:00:00Z date_updated: 2026-07-07T13:42:32Z day: '12' ddc: - '000' department: - _id: DaAl file: - access_level: open_access checksum: 2aaaa7d7226e49161311d91627cf783b content_type: application/pdf creator: kschuh date_created: 2021-05-25T09:51:36Z date_updated: 2021-05-25T09:51:36Z file_id: '9421' file_name: 2020_PMLR_Kurtz.pdf file_size: 741899 relation: main_file success: 1 file_date_updated: 2021-05-25T09:51:36Z has_accepted_license: '1' intvolume: ' 119' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 5533-5543 publication: 37th International Conference on Machine Learning publication_identifier: issn: - 2640-3498 quality_controlled: '1' scopus_import: '1' status: public title: Inducing and exploiting activation sparsity for fast neural network inference type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '8285' 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. 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). article_number: '043202' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Benjamin K. full_name: Malia, Benjamin K. last_name: Malia - first_name: Julián full_name: Martínez-Rincón, Julián last_name: Martínez-Rincón - first_name: Yunfan full_name: Wu, Yunfan last_name: Wu - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark A. full_name: Kasevich, Mark A. last_name: Kasevich citation: 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 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. 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. 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. mla: Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202. short: B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020). das_tickbox: '0' date_created: 2020-08-24T06:24:04Z date_published: 2020-07-24T00:00:00Z date_updated: 2026-07-08T08:56:44Z day: '24' department: - _id: OnHo doi: 10.1103/PhysRevLett.125.043202 external_id: arxiv: - '1912.10218' isi: - '000552227400008' pmid: - '32794788' intvolume: ' 125' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.10218 month: '07' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit type: journal_article user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d volume: 125 year: '2020' ... --- _id: '8319' abstract: - lang: eng text: We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. 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. 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. article_number: '012224' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yunfan full_name: Wu, Yunfan last_name: Wu - first_name: Rajiv full_name: Krishnakumar, Rajiv last_name: Krishnakumar - first_name: Julián full_name: Martínez-Rincón, Julián last_name: Martínez-Rincón - first_name: Benjamin K. full_name: Malia, Benjamin K. last_name: Malia - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark A. full_name: Kasevich, Mark A. last_name: Kasevich citation: ama: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224 apa: Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224 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. ieee: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020. 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. Physical Review A. 102(1), 012224. mla: Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224. short: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020). das_tickbox: '0' date_created: 2020-08-30T22:01:10Z date_published: 2020-07-30T00:00:00Z date_updated: 2026-07-08T08:59:02Z day: '30' department: - _id: OnHo doi: 10.1103/PhysRevA.102.012224 external_id: arxiv: - '1912.08334' isi: - '000555104200011' intvolume: ' 102' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.08334 month: '07' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Retrieval of cavity-generated atomic spin squeezing after free-space release type: journal_article user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d volume: 102 year: '2020' ... --- _id: '8127' abstract: - lang: eng text: Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. 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. 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. article_number: e56261 article_processing_charge: No article_type: original author: - first_name: Pedro J. full_name: Gonçalves, Pedro J. last_name: Gonçalves orcid: 0000-0002-6987-4836 - first_name: Jan-Matthis full_name: Lueckmann, Jan-Matthis last_name: Lueckmann orcid: 0000-0003-4320-4663 - first_name: Michael full_name: Deistler, Michael last_name: Deistler orcid: 0000-0002-3573-0404 - first_name: Marcel full_name: Nonnenmacher, Marcel last_name: Nonnenmacher orcid: 0000-0001-6044-6627 - first_name: Kaan full_name: Öcal, Kaan last_name: Öcal orcid: 0000-0002-8528-6858 - first_name: Giacomo full_name: Bassetto, Giacomo last_name: Bassetto - first_name: Chaitanya full_name: Chintaluri, Chaitanya id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E last_name: Chintaluri orcid: 0000-0003-4252-1608 - first_name: William F. full_name: Podlaski, William F. last_name: Podlaski orcid: 0000-0001-6619-7502 - first_name: Sara A. full_name: Haddad, Sara A. last_name: Haddad orcid: 0000-0003-0807-0823 - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: David S. full_name: Greenberg, David S. last_name: Greenberg - first_name: Jakob H. full_name: Macke, Jakob H. last_name: Macke orcid: 0000-0001-5154-8912 citation: 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 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 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. 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. 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. 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. 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). das_tickbox: '1' date_created: 2020-07-16T12:26:04Z date_published: 2020-09-17T00:00:00Z date_updated: 2026-07-13T12:31:21Z day: '17' ddc: - '570' department: - _id: TiVo doi: 10.7554/eLife.56261 ec_funded: 1 external_id: isi: - '000584989400001' pmid: - '32940606' file: - access_level: open_access checksum: c4300ddcd93ed03fc9c6cdf1f77890be content_type: application/pdf creator: cziletti date_created: 2020-10-27T11:37:32Z date_updated: 2020-10-27T11:37:32Z file_id: '8709' file_name: 2020_eLife_Gonçalves.pdf file_size: 17355867 relation: main_file success: 1 file_date_updated: 2020-10-27T11:37:32Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Training deep neural density estimators to identify mechanistic models of neural dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2020' ... --- OA_place: repository OA_type: green _id: '22166' 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). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jacob full_name: Fox, Jacob last_name: Fox - first_name: Xiaoyu full_name: He, Xiaoyu last_name: He - first_name: Yuval full_name: Wigderson, Yuval id: 2d0023a0-1567-11f0-833d-d5c1e476d4b5 last_name: Wigderson citation: ama: Fox J, He X, Wigderson Y. Ramsey, Paper, Scissors. Random Structures & Algorithms. 2020;57(4):1157-1173. doi:10.1002/rsa.20950 apa: Fox, J., He, X., & Wigderson, Y. (2020). Ramsey, Paper, Scissors. Random Structures & Algorithms. Wiley. https://doi.org/10.1002/rsa.20950 chicago: Fox, Jacob, Xiaoyu He, and Yuval Wigderson. “Ramsey, Paper, Scissors.” Random Structures & Algorithms. Wiley, 2020. https://doi.org/10.1002/rsa.20950. ieee: J. Fox, X. He, and Y. Wigderson, “Ramsey, Paper, Scissors,” Random Structures & Algorithms, vol. 57, no. 4. Wiley, pp. 1157–1173, 2020. ista: Fox J, He X, Wigderson Y. 2020. Ramsey, Paper, Scissors. Random Structures & Algorithms. 57(4), 1157–1173. 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. short: J. Fox, X. He, Y. Wigderson, Random Structures & Algorithms 57 (2020) 1157–1173. date_created: 2026-06-29T10:54:10Z date_published: 2020-12-01T00:00:00Z date_updated: 2026-07-14T08:31:05Z day: '01' doi: 10.1002/rsa.20950 extern: '1' external_id: arxiv: - '1906.01092' intvolume: ' 57' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1906.01092 month: '12' oa: 1 oa_version: Preprint page: 1157-1173 publication: Random Structures & Algorithms publication_identifier: eissn: - 1098-2418 issn: - 1042-9832 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Ramsey, Paper, Scissors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2020' ... --- OA_place: repository OA_type: green _id: '22182' abstract: - lang: eng text: We present a short new proof of the canonical polynomial van der Waerden theorem, recently established by Girão. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jacob full_name: Fox, Jacob last_name: Fox - first_name: Yuval full_name: Wigderson, Yuval id: 2d0023a0-1567-11f0-833d-d5c1e476d4b5 last_name: Wigderson - first_name: Yufei full_name: Zhao, Yufei last_name: Zhao citation: 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 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 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. 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. 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. short: J. Fox, Y. Wigderson, Y. Zhao, Comptes Rendus Mathématique 358 (2020) 957–959. date_created: 2026-06-29T11:00:09Z date_published: 2020-12-03T00:00:00Z date_updated: 2026-07-14T09:19:20Z day: '03' doi: 10.5802/crmath.101 extern: '1' external_id: arxiv: - '2005.04135' intvolume: ' 358' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2005.04135 mathsc: - 05D10 - 11B30 month: '12' oa: 1 oa_version: Preprint page: 957-959 publication: Comptes Rendus Mathématique publication_identifier: eissn: - 1778-3569 issn: - 1631-073X publication_status: published publisher: Académie des Sciences quality_controlled: '1' scopus_import: '1' status: public title: A short proof of the canonical polynomial van der Waerden theorem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 358 year: '2020' ... --- OA_place: repository OA_type: green _id: '22185' 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. 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 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. ieee: X. He and Y. Wigderson, “Multicolor Ramsey numbers via pseudorandom graphs,” The Electronic Journal of Combinatorics, vol. 27, no. 1. The Electronic Journal of Combinatorics, 2020. ista: He X, Wigderson Y. 2020. Multicolor Ramsey numbers via pseudorandom graphs. The Electronic Journal of Combinatorics. 27(1), P1.32. 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. short: X. He, Y. Wigderson, The Electronic Journal of Combinatorics 27 (2020). date_created: 2026-06-29T12:06:14Z date_published: 2020-02-01T00:00:00Z date_updated: 2026-07-14T09:42:53Z day: '01' doi: 10.37236/9071 extern: '1' external_id: arxiv: - '1910.06287' intvolume: ' 27' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1910.06287 mathsc: - 05C55 - 05D10 month: '02' oa: 1 oa_version: Preprint publication: The Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: The Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: Multicolor Ramsey numbers via pseudorandom graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2020' ...