[{"quality_controlled":"1","oa_version":"Published Version","_id":"9605","volume":189,"department":[{"_id":"HeEd"}],"scopus_import":"1","citation":{"ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2021. Computing the multicover bifiltration. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 27.","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">10.4230/LIPIcs.SoCG.2021.27</a>","apa":"Corbet, R., Kerber, M., Lesnick, M., &#38; Osang, G. F. (2021). Computing the multicover bifiltration. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">https://doi.org/10.4230/LIPIcs.SoCG.2021.27</a>","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” in <i>Leibniz International Proceedings in Informatics</i>, Online, 2021, vol. 189.","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” <i>Leibniz International Proceedings in Informatics</i>, vol. 189, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">10.4230/LIPIcs.SoCG.2021.27</a>.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">https://doi.org/10.4230/LIPIcs.SoCG.2021.27</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPIcs.SoCG.2021.27","author":[{"full_name":"Corbet, René","first_name":"René","last_name":"Corbet"},{"full_name":"Kerber, Michael","first_name":"Michael","last_name":"Kerber"},{"full_name":"Lesnick, Michael","last_name":"Lesnick","first_name":"Michael"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","first_name":"Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang"}],"title":"Computing the multicover bifiltration","date_updated":"2025-07-10T12:01:57Z","arxiv":1,"day":"02","file_date_updated":"2021-06-28T12:40:47Z","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771849"]},"related_material":{"link":[{"url":"https://arxiv.org/abs/2103.07823","relation":"extended_version"}],"record":[{"relation":"later_version","id":"12709","status":"public"}]},"acknowledgement":"The authors want to thank the reviewers for many helpful comments and suggestions.","external_id":{"arxiv":["2103.07823"]},"conference":{"name":"SoCG: International Symposium on Computational Geometry","location":"Online","start_date":"2021-06-07","end_date":"2021-06-11"},"status":"public","publication":"Leibniz International Proceedings in Informatics","ddc":["516"],"month":"06","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2021-06-27T22:01:49Z","abstract":[{"text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. ","lang":"eng"}],"has_accepted_license":"1","alternative_title":["LIPIcs"],"intvolume":"       189","language":[{"iso":"eng"}],"file":[{"creator":"cziletti","checksum":"0de217501e7ba8b267d58deed0d51761","file_name":"2021_LIPIcs_Corbet.pdf","date_created":"2021-06-28T12:40:47Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":"1367983","file_id":"9610","success":1,"date_updated":"2021-06-28T12:40:47Z"}],"publication_status":"published","article_processing_charge":"No","year":"2021","date_published":"2021-06-02T00:00:00Z","article_number":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"conference"},{"author":[{"last_name":"Tononi","first_name":"A.","full_name":"Tononi, A."},{"full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto","last_name":"Cappellaro","orcid":"0000-0001-6110-2359"},{"last_name":"Bighin","orcid":"0000-0001-8823-9777","first_name":"Giacomo","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Salasnich","first_name":"L.","full_name":"Salasnich, L."}],"title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","date_updated":"2025-07-10T12:01:58Z","day":"01","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","article_type":"letter_note","arxiv":1,"external_id":{"arxiv":["2009.06491"],"isi":["000662296700014"]},"_id":"9606","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06491"}],"scopus_import":"1","department":[{"_id":"MiLe"}],"volume":103,"doi":"10.1103/PhysRevA.103.L061303","citation":{"ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. <i>Physical Review A</i>. 2021;103(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">10.1103/PhysRevA.103.L061303</a>","ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","apa":"Tononi, A., Cappellaro, A., Bighin, G., &#38; Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">https://doi.org/10.1103/PhysRevA.103.L061303</a>","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” <i>Physical Review A</i>, vol. 103, no. 6. American Physical Society, 2021.","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” <i>Physical Review A</i>, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">10.1103/PhysRevA.103.L061303</a>.","short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">https://doi.org/10.1103/PhysRevA.103.L061303</a>."},"publication_status":"published","year":"2021","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"L061303","date_published":"2021-06-01T00:00:00Z","isi":1,"type":"journal_article","oa":1,"issue":"6","status":"public","month":"06","publication":"Physical Review A","abstract":[{"lang":"eng","text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results."}],"date_created":"2021-06-27T22:01:49Z","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":"       103"},{"oa":1,"isi":1,"type":"journal_article","file":[{"file_id":"9609","success":1,"date_updated":"2021-06-28T11:35:30Z","relation":"main_file","date_created":"2021-06-28T11:35:30Z","checksum":"885b746051a7a6b6e24e3d2781a48fde","creator":"asandaue","file_name":"2021_ELife_Bespalov.pdf","file_size":2500720,"content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","year":"2021","article_processing_charge":"No","date_published":"2021-05-24T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"eLife Sciences Publications","abstract":[{"text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use.","lang":"eng"}],"has_accepted_license":"1","pmid":1,"date_created":"2021-06-27T22:01:49Z","intvolume":"        10","language":[{"iso":"eng"}],"ddc":["570"],"publication":"eLife","status":"public","month":"05","day":"24","article_type":"original","file_date_updated":"2021-06-28T11:35:30Z","acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","publication_identifier":{"eissn":["2050-084X"]},"external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"author":[{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"first_name":"René","last_name":"Bernard","full_name":"Bernard, René"},{"full_name":"Gilis, Anja","first_name":"Anja","last_name":"Gilis"},{"full_name":"Gerlach, Björn","first_name":"Björn","last_name":"Gerlach"},{"full_name":"Guillén, Javier","last_name":"Guillén","first_name":"Javier"},{"last_name":"Castagné","first_name":"Vincent","full_name":"Castagné, Vincent"},{"last_name":"Lefevre","first_name":"Isabel A.","full_name":"Lefevre, Isabel A."},{"full_name":"Ducrey, Fiona","last_name":"Ducrey","first_name":"Fiona"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"full_name":"Bongiovanni, Sandrine","first_name":"Sandrine","last_name":"Bongiovanni"},{"last_name":"Altevogt","first_name":"Bruce","full_name":"Altevogt, Bruce"},{"last_name":"Arroyo-Araujo","first_name":"María","full_name":"Arroyo-Araujo, María"},{"full_name":"Bikovski, Lior","last_name":"Bikovski","first_name":"Lior"},{"full_name":"De Bruin, Natasja","first_name":"Natasja","last_name":"De Bruin"},{"full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez","first_name":"Esmeralda"},{"full_name":"Dityatev, Alexander","last_name":"Dityatev","first_name":"Alexander"},{"full_name":"Emmerich, Christoph H.","first_name":"Christoph H.","last_name":"Emmerich"},{"full_name":"Fares, Raafat","last_name":"Fares","first_name":"Raafat"},{"full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham","first_name":"Chantelle"},{"last_name":"Froger-Colléaux","first_name":"Christelle","full_name":"Froger-Colléaux, Christelle"},{"full_name":"Gailus-Durner, Valerie","first_name":"Valerie","last_name":"Gailus-Durner"},{"last_name":"Hölter","first_name":"Sabine M.","full_name":"Hölter, Sabine M."},{"first_name":"Martine Cj","last_name":"Hofmann","full_name":"Hofmann, Martine Cj"},{"full_name":"Kabitzke, Patricia","first_name":"Patricia","last_name":"Kabitzke"},{"last_name":"Kas","first_name":"Martien Jh","full_name":"Kas, Martien Jh"},{"last_name":"Kurreck","first_name":"Claudia","full_name":"Kurreck, Claudia"},{"last_name":"Moser","first_name":"Paul","full_name":"Moser, Paul"},{"full_name":"Pietraszek, Malgorzata","first_name":"Malgorzata","last_name":"Pietraszek"},{"full_name":"Popik, Piotr","first_name":"Piotr","last_name":"Popik"},{"full_name":"Potschka, Heidrun","first_name":"Heidrun","last_name":"Potschka"},{"first_name":"Ernesto","last_name":"Prado Montes De Oca","full_name":"Prado Montes De Oca, Ernesto"},{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"full_name":"Riedel, Gernot","first_name":"Gernot","last_name":"Riedel"},{"full_name":"Ritskes-Hoitinga, Merel","last_name":"Ritskes-Hoitinga","first_name":"Merel"},{"last_name":"Samardzic","first_name":"Janko","full_name":"Samardzic, Janko"},{"first_name":"Michael","last_name":"Schunn","orcid":"0000-0003-4326-5300","full_name":"Schunn, Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stöger, Claudia","first_name":"Claudia","last_name":"Stöger"},{"full_name":"Voikar, Vootele","first_name":"Vootele","last_name":"Voikar"},{"first_name":"Jan","last_name":"Vollert","full_name":"Vollert, Jan"},{"full_name":"Wever, Kimberley E.","last_name":"Wever","first_name":"Kimberley E."},{"full_name":"Wuyts, Kathleen","first_name":"Kathleen","last_name":"Wuyts"},{"full_name":"Macleod, Malcolm R.","last_name":"Macleod","first_name":"Malcolm R."},{"full_name":"Dirnagl, Ulrich","first_name":"Ulrich","last_name":"Dirnagl"},{"full_name":"Steckler, Thomas","last_name":"Steckler","first_name":"Thomas"}],"title":"Introduction to the EQIPD quality system","date_updated":"2026-04-02T13:55:57Z","volume":10,"department":[{"_id":"PreCl"}],"scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>.","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>, vol. 10, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>.","ieee":"A. Bespalov <i>et al.</i>, “Introduction to the EQIPD quality system,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021."},"doi":"10.7554/eLife.63294","quality_controlled":"1","oa_version":"Published Version","_id":"9607"},{"external_id":{"isi":["000636043400048"],"arxiv":["2012.12276"],"pmid":["33632894"]},"file_date_updated":"2021-09-23T14:00:05Z","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_type":"original","acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","day":"26","arxiv":1,"date_updated":"2025-04-14T07:52:05Z","title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","author":[{"full_name":"Bluvstein, D.","last_name":"Bluvstein","first_name":"D."},{"first_name":"A.","last_name":"Omran","full_name":"Omran, A."},{"full_name":"Levine, H.","last_name":"Levine","first_name":"H."},{"last_name":"Keesling","first_name":"A.","full_name":"Keesling, A."},{"full_name":"Semeghini, G.","first_name":"G.","last_name":"Semeghini"},{"last_name":"Ebadi","first_name":"S.","full_name":"Ebadi, S."},{"full_name":"Wang, T. T.","last_name":"Wang","first_name":"T. T."},{"first_name":"Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"full_name":"Maskara, N.","last_name":"Maskara","first_name":"N."},{"full_name":"Ho, W. W.","last_name":"Ho","first_name":"W. W."},{"first_name":"S.","last_name":"Choi","full_name":"Choi, S."},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"full_name":"Greiner, M.","last_name":"Greiner","first_name":"M."},{"first_name":"V.","last_name":"Vuletić","full_name":"Vuletić, V."},{"full_name":"Lukin, M. D.","last_name":"Lukin","first_name":"M. D."}],"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"citation":{"chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” <i>Science</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/science.abg2530\">https://doi.org/10.1126/science.abg2530</a>.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359.","mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” <i>Science</i>, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:<a href=\"https://doi.org/10.1126/science.abg2530\">10.1126/science.abg2530</a>.","ieee":"D. Bluvstein <i>et al.</i>, “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” <i>Science</i>, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.abg2530\">https://doi.org/10.1126/science.abg2530</a>","ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359.","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. <i>Science</i>. 2021;371(6536):1355-1359. doi:<a href=\"https://doi.org/10.1126/science.abg2530\">10.1126/science.abg2530</a>"},"doi":"10.1126/science.abg2530","department":[{"_id":"MaSe"}],"scopus_import":"1","volume":371,"_id":"9618","quality_controlled":"1","oa_version":"Preprint","type":"journal_article","ec_funded":1,"isi":1,"oa":1,"page":"1355-1359","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-03-26T00:00:00Z","keyword":["Multidisciplinary"],"year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf","creator":"patrickd","date_created":"2021-09-23T14:00:05Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3671159,"file_id":"10040","success":1,"date_updated":"2021-09-23T14:00:05Z"}],"language":[{"iso":"eng"}],"intvolume":"       371","has_accepted_license":"1","date_created":"2021-06-29T12:04:05Z","pmid":1,"abstract":[{"lang":"eng","text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science."}],"publisher":"AAAS","ddc":["539"],"month":"03","publication":"Science","status":"public","issue":"6536"},{"author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter","orcid":"0000-0002-5646-9524","last_name":"Davies","first_name":"Peter"}],"date_updated":"2025-09-10T10:04:46Z","title":"Collecting coupons is faster with friends","file_date_updated":"2021-07-01T11:21:40Z","acknowledgement":"Peter Davies is supported by the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","publication_identifier":{"eisbn":["9783030795276"],"isbn":["9783030795269"],"issn":["0302-9743"],"eissn":["1611-3349"]},"day":"20","conference":{"end_date":"2021-07-01","start_date":"2021-06-28","name":"SIROCCO: International Colloquium on Structural Information and Communication Complexity","location":"Wrocław, Poland"},"external_id":{"isi":["001292788400001"]},"_id":"9620","quality_controlled":"1","oa_version":"Preprint","scopus_import":"1","department":[{"_id":"DaAl"}],"volume":12810,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"D.-A. Alistarh, P. Davies, in:, Structural Information and Communication Complexity, Springer Nature, 2021, pp. 3–12.","chicago":"Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with Friends.” In <i>Structural Information and Communication Complexity</i>, 12810:3–12. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">https://doi.org/10.1007/978-3-030-79527-6_1</a>.","apa":"Alistarh, D.-A., &#38; Davies, P. (2021). Collecting coupons is faster with friends. In <i>Structural Information and Communication Complexity</i> (Vol. 12810, pp. 3–12). Wrocław, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">https://doi.org/10.1007/978-3-030-79527-6_1</a>","ista":"Alistarh D-A, Davies P. 2021. Collecting coupons is faster with friends. Structural Information and Communication Complexity. SIROCCO: International Colloquium on Structural Information and Communication Complexity, LNCS, vol. 12810, 3–12.","ama":"Alistarh D-A, Davies P. Collecting coupons is faster with friends. In: <i>Structural Information and Communication Complexity</i>. Vol 12810. Springer Nature; 2021:3-12. doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">10.1007/978-3-030-79527-6_1</a>","mla":"Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with Friends.” <i>Structural Information and Communication Complexity</i>, vol. 12810, Springer Nature, 2021, pp. 3–12, doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">10.1007/978-3-030-79527-6_1</a>.","ieee":"D.-A. Alistarh and P. Davies, “Collecting coupons is faster with friends,” in <i>Structural Information and Communication Complexity</i>, Wrocław, Poland, 2021, vol. 12810, pp. 3–12."},"doi":"10.1007/978-3-030-79527-6_1","article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"file_id":"9621","date_updated":"2021-07-01T11:21:40Z","date_created":"2021-07-01T11:21:40Z","relation":"main_file","checksum":"fe37fb9af3f5016c1084af9d6e7109bd","creator":"pdavies","file_name":"Population_Coupon_Collector.pdf","file_size":319728,"access_level":"open_access","content_type":"application/pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2021-06-20T00:00:00Z","page":"3-12","isi":1,"type":"conference","ec_funded":1,"oa":1,"status":"public","publication":"Structural Information and Communication Complexity","ddc":["000"],"month":"06","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).\r\n\r\nWe provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons."}],"has_accepted_license":"1","date_created":"2021-07-01T11:04:43Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"     12810"},{"date_created":"2021-07-04T22:01:24Z","abstract":[{"text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors.","lang":"eng"}],"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"        20","month":"06","publication":"Materials Today Physics","status":"public","corr_author":"1","isi":1,"type":"journal_article","year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-06-03T00:00:00Z","article_number":"100452","department":[{"_id":"MaIb"}],"scopus_import":"1","volume":20,"doi":"10.1016/j.mtphys.2021.100452","citation":{"short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021).","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” <i>Materials Today Physics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">https://doi.org/10.1016/j.mtphys.2021.100452</a>.","ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. <i>Materials Today Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">https://doi.org/10.1016/j.mtphys.2021.100452</a>","ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. <i>Materials Today Physics</i>. 2021;20. doi:<a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">10.1016/j.mtphys.2021.100452</a>","ieee":"L. Su <i>et al.</i>, “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” <i>Materials Today Physics</i>, vol. 20. Elsevier, 2021.","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” <i>Materials Today Physics</i>, vol. 20, 100452, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">10.1016/j.mtphys.2021.100452</a>."},"_id":"9626","quality_controlled":"1","oa_version":"None","article_type":"original","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","publication_identifier":{"eissn":["2542-5293"]},"day":"03","external_id":{"isi":["000703159600010"]},"author":[{"full_name":"Su, Lizhong","first_name":"Lizhong","last_name":"Su"},{"full_name":"Hong, Tao","last_name":"Hong","first_name":"Tao"},{"full_name":"Wang, Dongyang","first_name":"Dongyang","last_name":"Wang"},{"last_name":"Wang","first_name":"Sining","full_name":"Wang, Sining"},{"last_name":"Qin","first_name":"Bingchao","full_name":"Qin, Bingchao"},{"full_name":"Zhang, Mengmeng","last_name":"Zhang","first_name":"Mengmeng"},{"last_name":"Gao","first_name":"Xiang","full_name":"Gao, Xiang"},{"first_name":"Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng"},{"first_name":"Li Dong","last_name":"Zhao","full_name":"Zhao, Li Dong"}],"date_updated":"2024-10-09T21:00:40Z","title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation"},{"date_created":"2021-07-04T22:01:24Z","abstract":[{"text":"We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum.","lang":"eng"}],"publisher":"Cambridge University Press","language":[{"iso":"eng"}],"intvolume":"        64","issue":"3","month":"08","ddc":["500"],"corr_author":"1","status":"public","publication":"Proceedings of the Edinburgh Mathematical Society","page":"443-447","type":"journal_article","isi":1,"oa":1,"year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-01T00:00:00Z","scopus_import":"1","department":[{"_id":"JaMa"}],"volume":64,"citation":{"chicago":"Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions of Bipartite Hamiltonians.” <i>Proceedings of the Edinburgh Mathematical Society</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/S0013091521000080\">https://doi.org/10.1017/S0013091521000080</a>.","short":"D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical Society 64 (2021) 443–447.","ieee":"D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite Hamiltonians,” <i>Proceedings of the Edinburgh Mathematical Society</i>, vol. 64, no. 3. Cambridge University Press, pp. 443–447, 2021.","mla":"Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” <i>Proceedings of the Edinburgh Mathematical Society</i>, vol. 64, no. 3, Cambridge University Press, 2021, pp. 443–47, doi:<a href=\"https://doi.org/10.1017/S0013091521000080\">10.1017/S0013091521000080</a>.","apa":"Lenz, D., Weinmann, T., &#38; Wirth, M. (2021). Self-adjoint extensions of bipartite Hamiltonians. <i>Proceedings of the Edinburgh Mathematical Society</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0013091521000080\">https://doi.org/10.1017/S0013091521000080</a>","ama":"Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians. <i>Proceedings of the Edinburgh Mathematical Society</i>. 2021;64(3):443-447. doi:<a href=\"https://doi.org/10.1017/S0013091521000080\">10.1017/S0013091521000080</a>","ista":"Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447."},"doi":"10.1017/S0013091521000080","_id":"9627","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0013091521000080"}],"quality_controlled":"1","oa_version":"Published Version","acknowledgement":"M. W. gratefully acknowledges financial support by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA GmbH for their financial support in the form of scholarships during his Master's and Bachelor's studies respectively. The authors want to thank Mark Malamud for pointing out the reference [1] to them. This work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.","publication_identifier":{"issn":["0013-0915"],"eissn":["1464-3839"]},"article_type":"original","day":"01","arxiv":1,"external_id":{"isi":["000721363700003"],"arxiv":["1912.03670"]},"author":[{"full_name":"Lenz, Daniel","first_name":"Daniel","last_name":"Lenz"},{"full_name":"Weinmann, Timon","first_name":"Timon","last_name":"Weinmann"},{"first_name":"Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"date_updated":"2026-06-18T19:54:27Z","title":"Self-adjoint extensions of bipartite Hamiltonians"},{"external_id":{"pmid":["34155381"],"isi":["000664016300003"]},"day":"21","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"article_type":"original","title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","date_updated":"2025-04-14T07:52:26Z","author":[{"last_name":"Yang","first_name":"Qiutan","full_name":"Yang, Qiutan"},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","first_name":"Shi-lei","last_name":"Xue"},{"last_name":"Chan","first_name":"Chii Jou","full_name":"Chan, Chii Jou"},{"full_name":"Rempfler, Markus","last_name":"Rempfler","first_name":"Markus"},{"last_name":"Vischi","first_name":"Dario","full_name":"Vischi, Dario"},{"full_name":"Maurer-Gutierrez, Francisca","first_name":"Francisca","last_name":"Maurer-Gutierrez"},{"full_name":"Hiiragi, Takashi","first_name":"Takashi","last_name":"Hiiragi"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"first_name":"Prisca","last_name":"Liberali","full_name":"Liberali, Prisca"}],"project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"}],"citation":{"chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","ieee":"Q. Yang <i>et al.</i>, “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” <i>Nature Cell Biology</i>, vol. 23. Springer Nature, pp. 733–744, 2021.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>, vol. 23, Springer Nature, 2021, pp. 733–744, doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>.","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. 2021;23:733–744. doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>"},"doi":"10.1038/s41556-021-00700-2","scopus_import":"1","department":[{"_id":"EdHa"}],"volume":23,"_id":"9629","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"isi":1,"ec_funded":1,"type":"journal_article","oa":1,"page":"733–744","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-06-21T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2021","language":[{"iso":"eng"}],"intvolume":"        23","abstract":[{"lang":"eng","text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis."}],"date_created":"2021-07-04T22:01:25Z","pmid":1,"publisher":"Springer Nature","publication":"Nature Cell Biology","month":"06","status":"public","corr_author":"1"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","date_created":"2021-07-07T20:43:10Z","department":[{"_id":"AnHi"}],"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"citation":{"ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","mla":"Higginbotham, Andrew P. <i>Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.”</i> Institute of Science and Technology Austria, 2021.","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021."},"status":"public","oa_version":"Submitted Version","_id":"9636","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10029"}]},"file_date_updated":"2021-07-07T20:37:28Z","oa":1,"type":"research_data","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P"}],"file":[{"access_level":"open_access","content_type":"application/zip","file_size":3345244,"checksum":"18e90687ec7bbd75f8bfea4d8293fb30","file_name":"figures_data.zip","creator":"ahigginb","date_created":"2021-07-07T20:37:28Z","relation":"main_file","date_updated":"2021-07-07T20:37:28Z","success":1,"file_id":"9637"}],"year":"2021","article_processing_charge":"No","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\"","date_published":"2021-01-01T00:00:00Z","date_updated":"2025-04-15T06:54:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":"        12","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","abstract":[{"text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.","lang":"eng"}],"date_created":"2021-07-11T22:01:15Z","pmid":1,"status":"public","ddc":["510"],"month":"06","publication":"Nature Communications","issue":"1","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","article_number":"4009","date_published":"2021-06-29T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"checksum":"5767418926a7f7fb76151de29473dae0","file_name":"2021_NatCoom_Tkadlec.pdf","creator":"cziletti","date_created":"2021-07-19T13:02:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":628992,"success":1,"file_id":"9692","date_updated":"2021-07-19T13:02:20Z"}],"article_processing_charge":"No","year":"2021","publication_status":"published","doi":"10.1038/s41467-021-24271-w","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>"},"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"volume":12,"department":[{"_id":"KrCh"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","_id":"9640","external_id":{"isi":["000671752100003"],"pmid":["34188036"]},"publication_identifier":{"eissn":["2041-1723"]},"file_date_updated":"2021-07-19T13:02:20Z","acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","article_type":"original","day":"29","date_updated":"2026-04-02T14:04:10Z","title":"Fast and strong amplifiers of natural selection","author":[{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}]},{"status":"public","month":"06","ddc":["610"],"publication":"Neurobiology of Learning and Memory","has_accepted_license":"1","date_created":"2021-07-11T22:01:16Z","pmid":1,"abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"       183","year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"date_updated":"2021-07-19T13:46:06Z","success":1,"file_id":"9694","content_type":"application/pdf","access_level":"open_access","file_size":1994793,"checksum":"8e8298a9e8c7df146ad23f32c2a63929","creator":"cziletti","file_name":"2021_NeurobLearnMemory_Fredes.pdf","relation":"main_file","date_created":"2021-07-19T13:46:06Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-30T00:00:00Z","article_number":"107486","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"_id":"9641","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"RySh"}],"scopus_import":"1","volume":183,"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"citation":{"short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. 2021;183. doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","apa":"Fredes, F., &#38; Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” <i>Neurobiology of Learning and Memory</i>, vol. 183. Elsevier, 2021.","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>, vol. 183, 107486, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>."},"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)"},"doi":"10.1016/j.nlm.2021.107486","author":[{"last_name":"Fredes","first_name":"Felipe","full_name":"Fredes, Felipe"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"}],"date_updated":"2025-07-10T12:02:00Z","title":"The role of hippocampal mossy cells in novelty detection","publication_identifier":{"eissn":["1095-9564"],"issn":["1074-7427"]},"article_type":"original","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","file_date_updated":"2021-07-19T13:46:06Z","day":"30","external_id":{"pmid":["34214666"],"isi":["000677694900004"]}},{"ec_funded":1,"type":"journal_article","isi":1,"oa":1,"article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"file_name":"2021_CellReports_Venturino.pdf","creator":"cziletti","checksum":"f056255f6d01fd9a86b5387635928173","date_created":"2021-07-19T13:32:17Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":56388540,"file_id":"9693","success":1,"date_updated":"2021-07-19T13:32:17Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-07-06T00:00:00Z","article_number":"109313","pmid":1,"date_created":"2021-07-11T22:01:16Z","abstract":[{"lang":"eng","text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain."}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"        36","issue":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publication":"Cell Reports","ddc":["570"],"month":"07","status":"public","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","description":"News on IST Homepage"}]},"article_type":"original","publication_identifier":{"eissn":["2211-1247"]},"acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","file_date_updated":"2021-07-19T13:32:17Z","day":"06","external_id":{"isi":["000670188500004"],"pmid":["34233180"]},"author":[{"orcid":"0000-0003-2356-9403","last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven","last_name":"Schulz","orcid":"0000-0001-5297-733X"},{"full_name":"De Jesús-Cortés, Héctor","last_name":"De Jesús-Cortés","first_name":"Héctor"},{"first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E"},{"first_name":"Balint","last_name":"Nagy","full_name":"Nagy, Balint","id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425"},{"last_name":"Reilly-Andújar","first_name":"Francis","full_name":"Reilly-Andújar, Francis"},{"full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","last_name":"Colombo","orcid":"0000-0001-9434-8902"},{"first_name":"Ryan J","last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","last_name":"Schoot Uiterkamp"},{"last_name":"Bear","first_name":"Mark F.","full_name":"Bear, Mark F."},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","first_name":"Sandra"}],"date_updated":"2026-04-03T09:46:05Z","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","department":[{"_id":"SaSi"}],"scopus_import":"1","volume":36,"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"citation":{"ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. 2021;36(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Miteva FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","ieee":"A. Venturino <i>et al.</i>, “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” <i>Cell Reports</i>, vol. 36, no. 1. Elsevier, 2021.","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>, vol. 36, no. 1, 109313, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Miteva, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.celrep.2021.109313","_id":"9642","quality_controlled":"1","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","abstract":[{"lang":"eng","text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters."}],"date_created":"2021-07-11T22:01:17Z","status":"public","month":"06","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","oa":1,"ec_funded":1,"isi":1,"type":"conference","page":"1033-1048","date_published":"2021-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","article_processing_charge":"No","publication_status":"published","doi":"10.1145/3453483.3454093","citation":{"short":"K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1033–48. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>.","ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1033-1048. doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., &#38; Zikelic, D. (2021). Proving non-termination by program reversal. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1033–1048). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>","ista":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1033–1048.","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1033–48, doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>."},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"scopus_import":"1","department":[{"_id":"KrCh"}],"main_file_link":[{"url":"https://arxiv.org/abs/2104.01189","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","_id":"9644","external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"conference":{"end_date":"2021-06-26","start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation","location":"Online"},"arxiv":1,"publication_identifier":{"isbn":["9781450383912"]},"related_material":{"record":[{"relation":"research_data","id":"15284","status":"public"},{"relation":"dissertation_contains","id":"14539","status":"public"}]},"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","day":"01","date_updated":"2026-04-07T13:27:55Z","title":"Proving non-termination by program reversal","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Ehsan Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","first_name":"Petr","last_name":"Novotný"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699"}]},{"status":"public","month":"06","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","date_created":"2021-07-11T22:01:17Z","abstract":[{"lang":"eng","text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods."}],"date_published":"2021-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","year":"2021","publication_status":"published","oa":1,"ec_funded":1,"type":"conference","isi":1,"page":"772-787","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03183862/","open_access":"1"}],"oa_version":"Submitted Version","quality_controlled":"1","_id":"9645","citation":{"short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 772–87. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>.","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:772-787. doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., &#38; Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 772–787). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 772–87, doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>.","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 772–787."},"doi":"10.1145/3453483.3454076","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"}],"scopus_import":"1","date_updated":"2025-07-10T12:02:00Z","title":"Polynomial reachability witnesses via Stellensätze","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"full_name":"Mahdavi, Mohammad","first_name":"Mohammad","last_name":"Mahdavi"}],"external_id":{"isi":["000723661700050"]},"conference":{"location":"Online","name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20","end_date":"2021-06-26"},"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","publication_identifier":{"isbn":["9781450383912"]},"day":"01"},{"language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","abstract":[{"text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.","lang":"eng"}],"date_created":"2021-07-11T22:01:18Z","status":"public","month":"06","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","oa":1,"ec_funded":1,"type":"conference","isi":1,"page":"1171-1186","date_published":"2021-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","article_processing_charge":"No","publication_status":"published","citation":{"chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1171–86. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1171–86, doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1171-1186. doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1171–1186). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186."},"doi":"10.1145/3453483.3454102","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"scopus_import":"1","department":[{"_id":"KrCh"}],"main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","_id":"9646","external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"conference":{"name":"PLDI: Programming Language Design and Implementation","location":"Online","start_date":"2021-06-20","end_date":"2021-06-26"},"arxiv":1,"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","publication_identifier":{"isbn":["9781450383912"]},"day":"01","date_updated":"2025-04-15T07:55:05Z","title":"Quantitative analysis of assertion violations in probabilistic programs","author":[{"first_name":"Jinyi","last_name":"Wang","full_name":"Wang, Jinyi"},{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}]},{"external_id":{"isi":["000710180500002"]},"day":"04","file_date_updated":"2022-05-12T12:13:27Z","publication_identifier":{"issn":["0304-3975"]},"article_type":"original","acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","title":"Long lived transients in gene regulation","date_updated":"2025-04-15T06:25:56Z","author":[{"full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana"},{"id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia"},{"first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. 2021;893:1-16. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., &#38; Guet, C. C. (2021). Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” <i>Theoretical Computer Science</i>, vol. 893. Elsevier, pp. 1–16, 2021.","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>, vol. 893, Elsevier, 2021, pp. 1–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>."},"doi":"10.1016/j.tcs.2021.05.023","project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"volume":893,"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","_id":"9647","oa":1,"type":"journal_article","isi":1,"page":"1-16","date_published":"2021-06-04T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2022-05-12T12:13:27Z","success":1,"file_id":"11364","file_size":2566504,"access_level":"open_access","content_type":"application/pdf","date_created":"2022-05-12T12:13:27Z","relation":"main_file","creator":"dernst","checksum":"d3aef34cfb13e53bba4cf44d01680793","file_name":"2021_TheoreticalComputerScience_Petrov.pdf"}],"publication_status":"published","article_processing_charge":"No","year":"2021","intvolume":"       893","language":[{"iso":"eng"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof."}],"date_created":"2021-07-11T22:01:18Z","has_accepted_license":"1","publication":"Theoretical Computer Science","status":"public","corr_author":"1","month":"06","ddc":["004"]},{"date_updated":"2025-04-14T07:45:00Z","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","author":[{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"first_name":"Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin"},{"last_name":"Alotaibi","first_name":"SS","full_name":"Alotaibi, SS"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"external_id":{"pmid":["34254313"],"isi":["000680587100001"]},"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"article_type":"original","acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","file_date_updated":"2021-10-07T13:42:47Z","day":"01","_id":"9656","oa_version":"Published Version","quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>."},"doi":"10.1111/nph.17617","scopus_import":"1","department":[{"_id":"JiFr"}],"volume":232,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-10-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","year":"2021","publication_status":"published","file":[{"success":1,"file_id":"10105","date_updated":"2021-10-07T13:42:47Z","relation":"main_file","date_created":"2021-10-07T13:42:47Z","creator":"kschuh","checksum":"6422a6eb329b52d96279daaee0fcf189","file_name":"2021_NewPhytologist_Han.pdf","file_size":1939800,"content_type":"application/pdf","access_level":"open_access"}],"type":"journal_article","isi":1,"ec_funded":1,"oa":1,"page":"510-522","corr_author":"1","publication":"New Phytologist","ddc":["580"],"month":"10","status":"public","issue":"2","language":[{"iso":"eng"}],"intvolume":"       232","abstract":[{"lang":"eng","text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment."}],"pmid":1,"date_created":"2021-07-14T15:29:14Z","has_accepted_license":"1","publisher":"Wiley"},{"author":[{"full_name":"Gao, Z","first_name":"Z","last_name":"Gao"},{"full_name":"Chen, Z","last_name":"Chen","first_name":"Z"},{"first_name":"Y","last_name":"Cui","full_name":"Cui, Y"},{"last_name":"Ke","first_name":"M","full_name":"Ke, M"},{"full_name":"Xu, H","last_name":"Xu","first_name":"H"},{"first_name":"Q","last_name":"Xu","full_name":"Xu, Q"},{"full_name":"Chen, J","first_name":"J","last_name":"Chen"},{"full_name":"Li, Y","first_name":"Y","last_name":"Li"},{"full_name":"Huang, L","last_name":"Huang","first_name":"L"},{"full_name":"Zhao, H","first_name":"H","last_name":"Zhao"},{"full_name":"Huang, D","first_name":"D","last_name":"Huang"},{"full_name":"Mai, S","first_name":"S","last_name":"Mai"},{"first_name":"T","last_name":"Xu","full_name":"Xu, T"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Guan, Y","first_name":"Y","last_name":"Guan"},{"full_name":"Yang, W","first_name":"W","last_name":"Yang"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J","last_name":"Petrášek","full_name":"Petrášek, J"},{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"},{"last_name":"Chen","first_name":"X","full_name":"Chen, X"}],"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","date_updated":"2024-10-21T06:02:03Z","day":"07","article_type":"original","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"file_date_updated":"2021-07-19T12:13:34Z","external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"oa_version":"Published Version","quality_controlled":"1","_id":"9657","volume":33,"scopus_import":"1","department":[{"_id":"JiFr"}],"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)"},"doi":"10.1093/plcell/koab183","citation":{"chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>"},"file":[{"date_updated":"2021-07-19T12:13:34Z","success":1,"file_id":"9691","file_size":10566921,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-07-19T12:13:34Z","creator":"cziletti","checksum":"6715712ec306c321f0204c817b7f8ae7","file_name":"2021_PlantCell_Gao.pdf"}],"publication_status":"published","article_processing_charge":"No","year":"2021","date_published":"2021-07-07T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"2981–3003","oa":1,"isi":1,"type":"journal_article","issue":"9","publication":"Plant Cell","status":"public","ddc":["580"],"month":"07","publisher":"American Society of Plant Biologists","abstract":[{"text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.","lang":"eng"}],"pmid":1,"has_accepted_license":"1","date_created":"2021-07-14T15:32:43Z","intvolume":"        33","language":[{"iso":"eng"}]},{"issue":"1","status":"public","ddc":["530","540"],"month":"01","publication":"Nature Communications","abstract":[{"lang":"eng","text":"The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations."}],"has_accepted_license":"1","date_created":"2021-07-15T13:48:13Z","pmid":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        12","article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"success":1,"file_id":"9670","date_updated":"2021-07-15T13:55:46Z","creator":"asandaue","file_name":"2021_NatureCommunications_Reinhardt.pdf","checksum":"8b5e1fbe2f1ab936047008043150e894","date_created":"2021-07-15T13:55:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":1180227}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_number":"588","date_published":"2021-01-26T00:00:00Z","type":"journal_article","oa":1,"_id":"9669","extern":"1","oa_version":"Published Version","quality_controlled":"1","scopus_import":"1","volume":12,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-020-20821-w","citation":{"mla":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” <i>Nature Communications</i>, vol. 12, no. 1, 588, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-020-20821-w\">10.1038/s41467-020-20821-w</a>.","ieee":"A. Reinhardt and B. Cheng, “Quantum-mechanical exploration of the phase diagram of water,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ista":"Reinhardt A, Cheng B. 2021. Quantum-mechanical exploration of the phase diagram of water. Nature Communications. 12(1), 588.","ama":"Reinhardt A, Cheng B. Quantum-mechanical exploration of the phase diagram of water. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-20821-w\">10.1038/s41467-020-20821-w</a>","apa":"Reinhardt, A., &#38; Cheng, B. (2021). Quantum-mechanical exploration of the phase diagram of water. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20821-w\">https://doi.org/10.1038/s41467-020-20821-w</a>","chicago":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-020-20821-w\">https://doi.org/10.1038/s41467-020-20821-w</a>.","short":"A. Reinhardt, B. Cheng, Nature Communications 12 (2021)."},"author":[{"full_name":"Reinhardt, Aleks","first_name":"Aleks","last_name":"Reinhardt"},{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"}],"date_updated":"2023-02-23T14:04:20Z","title":"Quantum-mechanical exploration of the phase diagram of water","file_date_updated":"2021-07-15T13:55:46Z","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","day":"26","arxiv":1,"external_id":{"arxiv":["2010.13729"],"pmid":["33500405"]}},{"type":"journal_article","ec_funded":1,"isi":1,"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-06-23T00:00:00Z","article_number":"065009","publication_status":"published","year":"2021","article_processing_charge":"Yes","file":[{"file_id":"9690","success":1,"date_updated":"2021-07-19T11:47:16Z","file_name":"2021_NewJPhys_Huber.pdf","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","creator":"cziletti","date_created":"2021-07-19T11:47:16Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":3868445}],"language":[{"iso":"eng"}],"intvolume":"        23","abstract":[{"lang":"eng","text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment."}],"has_accepted_license":"1","date_created":"2021-07-18T22:01:22Z","publisher":"IOP Publishing","status":"public","ddc":["530"],"month":"06","publication":"New Journal of Physics","issue":"6","external_id":{"arxiv":["2102.04961"],"isi":["000664736300001"]},"day":"23","publication_identifier":{"eissn":["1367-2630"]},"acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","file_date_updated":"2021-07-19T11:47:16Z","article_type":"original","arxiv":1,"title":"Morphology of three-body quantum states from machine learning","date_updated":"2026-04-02T14:01:49Z","author":[{"last_name":"Huber","first_name":"David","full_name":"Huber, David"},{"first_name":"Oleksandr V.","last_name":"Marchukov","full_name":"Marchukov, Oleksandr V."},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1088/1367-2630/ac0576","department":[{"_id":"MiLe"}],"scopus_import":"1","volume":23,"_id":"9679","oa_version":"Published Version","quality_controlled":"1"}]