[{"arxiv":1,"abstract":[{"lang":"eng","text":"We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."}],"title":"Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation","department":[{"_id":"KrPi"},{"_id":"KrCh"}],"publication":"SIROCCO 2023: Structural Information and Communication Complexity ","publisher":"Springer Nature","oa_version":"Preprint","ec_funded":1,"date_created":"2023-07-16T22:01:12Z","oa":1,"acknowledgement":"We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021–2024.","status":"public","external_id":{"arxiv":["2204.13459"]},"citation":{"ama":"Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In: <i>SIROCCO 2023: Structural Information and Communication Complexity </i>. Vol 13892. Springer Nature; 2023:576-594. doi:<a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">10.1007/978-3-031-32733-9_26</a>","ista":"Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023: Structural Information and Communication Complexity . SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 576–594.","mla":"Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” <i>SIROCCO 2023: Structural Information and Communication Complexity </i>, vol. 13892, Springer Nature, 2023, pp. 576–94, doi:<a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">10.1007/978-3-031-32733-9_26</a>.","short":"S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information and Communication Complexity , Springer Nature, 2023, pp. 576–594.","ieee":"S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” in <i>SIROCCO 2023: Structural Information and Communication Complexity </i>, Alcala de Henares, Spain, 2023, vol. 13892, pp. 576–594.","chicago":"Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” In <i>SIROCCO 2023: Structural Information and Communication Complexity </i>, 13892:576–94. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">https://doi.org/10.1007/978-3-031-32733-9_26</a>.","apa":"Schmid, S., Svoboda, J., &#38; Yeo, M. X. (2023). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In <i>SIROCCO 2023: Structural Information and Communication Complexity </i> (Vol. 13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-32733-9_26\">https://doi.org/10.1007/978-3-031-32733-9_26</a>"},"publication_identifier":{"isbn":["9783031327322"],"eissn":["1611-3349"],"issn":["0302-9743"]},"page":"576-594","volume":13892,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13238","year":"2023","date_published":"2023-05-25T00:00:00Z","author":[{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","first_name":"Jakub"},{"first_name":"Michelle X","last_name":"Yeo","orcid":"0009-0001-3676-4809","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1007/978-3-031-32733-9_26","alternative_title":["LNCS"],"date_updated":"2025-07-14T09:09:53Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14506"}]},"article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","conference":{"start_date":"2023-06-06","location":"Alcala de Henares, Spain","end_date":"2023-06-09","name":"SIROCCO: Structural Information and Communication Complexity"},"day":"25","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"05","intvolume":"     13892","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.13459","open_access":"1"}],"publication_status":"published"},{"file_date_updated":"2023-07-19T06:55:39Z","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"},"date_published":"2023-07-05T00:00:00Z","author":[{"id":"0c5ff007-2600-11ee-b896-98bd8d663294","full_name":"Wei, Yujing","orcid":"0000-0001-8913-9719","last_name":"Wei","first_name":"Yujing"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"},{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"last_name":"Bakr","first_name":"Osman M.","full_name":"Bakr, Osman M."},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alpichshev","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek"}],"date_updated":"2023-07-19T06:59:19Z","doi":"10.1021/acs.jpclett.3c01158","article_processing_charge":"Yes (via OA deal)","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"        14","publication_status":"published","file":[{"file_size":2121252,"checksum":"c0c040063f06a51b9c463adc504f1a23","file_name":"2023_JourPhysChemistry_Wei.pdf","date_updated":"2023-07-19T06:55:39Z","file_id":"13253","content_type":"application/pdf","date_created":"2023-07-19T06:55:39Z","success":1,"relation":"main_file","access_level":"open_access","creator":"dernst"}],"day":"05","ddc":["530"],"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"07","isi":1,"title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"publication":"The Journal of Physical Chemistry Letters","publisher":"American Chemical Society","oa_version":"Published Version","ec_funded":1,"date_created":"2023-07-18T11:13:17Z","arxiv":1,"abstract":[{"lang":"eng","text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy."}],"page":"6309-6314","volume":14,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13251","year":"2023","has_accepted_license":"1","oa":1,"status":"public","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","article_type":"original","external_id":{"isi":["001022811500001"],"arxiv":["2304.14198"]},"issue":"27","citation":{"ieee":"Y. Wei <i>et al.</i>, “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., &#38; Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. 2023;14(27):6309-6314. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314."},"publication_identifier":{"eissn":["1948-7185"]}},{"publisher":"Springer Nature","publication":"npj Climate and Atmospheric Science","title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","department":[{"_id":"CaMu"}],"date_created":"2023-07-23T22:01:10Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":6,"year":"2023","has_accepted_license":"1","_id":"13256","external_id":{"isi":["001024920300002"]},"article_type":"original","oa":1,"acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","status":"public","publication_identifier":{"eissn":["2397-3722"]},"citation":{"ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>npj Climate and Atmospheric Science</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>, vol. 6, 82, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>.","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>.","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” <i>npj Climate and Atmospheric Science</i>, vol. 6. Springer Nature, 2023.","apa":"GOSWAMI, B. B., &#38; An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>Npj Climate and Atmospheric Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>"},"article_number":"82","file_date_updated":"2023-07-31T08:00:01Z","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"},"article_processing_charge":"Yes","doi":"10.1038/s41612-023-00411-5","date_updated":"2023-08-02T06:38:07Z","author":[{"last_name":"Goswami","first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"Goswami, Bidyut B"},{"full_name":"An, Soon Il","last_name":"An","first_name":"Soon Il"}],"date_published":"2023-07-08T00:00:00Z","quality_controlled":"1","scopus_import":"1","file":[{"content_type":"application/pdf","date_created":"2023-07-31T08:00:01Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_size":1750712,"checksum":"e9967d436a83b8ffcc6f58782e1f7500","file_name":"2023_npjclimate_Goswami.pdf","date_updated":"2023-07-31T08:00:01Z","file_id":"13326"}],"publication_status":"published","intvolume":"         6","ddc":["550"],"day":"08","isi":1,"month":"07","language":[{"iso":"eng"}]},{"issue":"3","external_id":{"arxiv":["2208.10038"],"isi":["001062708600002"]},"article_type":"original","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","oa":1,"status":"public","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"citation":{"apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., &#38; Modic, K. A. (2023). Magnetotropic susceptibility. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” <i>Physical Review B</i>, vol. 108, no. 3. American Physical Society, 2023.","chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>.","mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” <i>Physical Review B</i>, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>.","short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. <i>Physical Review B</i>. 2023;108(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":108,"year":"2023","_id":"13257","arxiv":1,"abstract":[{"text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.","lang":"eng"}],"publisher":"American Physical Society","publication":"Physical Review B","title":"Magnetotropic susceptibility","department":[{"_id":"KiMo"}],"date_created":"2023-07-23T22:01:10Z","oa_version":"Preprint","day":"15","isi":1,"month":"07","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"       108","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.10038"}],"article_processing_charge":"No","date_updated":"2023-12-13T11:58:57Z","doi":"10.1103/PhysRevB.108.035111","date_published":"2023-07-15T00:00:00Z","author":[{"full_name":"Shekhter, A.","first_name":"A.","last_name":"Shekhter"},{"first_name":"R. D.","last_name":"Mcdonald","full_name":"Mcdonald, R. D."},{"full_name":"Ramshaw, B. J.","last_name":"Ramshaw","first_name":"B. J."},{"orcid":"0000-0001-9760-3147","last_name":"Modic","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A"}],"quality_controlled":"1","scopus_import":"1","article_number":"035111"},{"_id":"13258","has_accepted_license":"1","year":"2023","volume":14,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>.","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>.","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>"},"publication_identifier":{"eissn":["2041-1723"]},"oa":1,"status":"public","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","external_id":{"pmid":["37438341"],"isi":["001029450400031"]},"article_type":"original","date_created":"2023-07-23T22:01:11Z","ec_funded":1,"oa_version":"Published Version","publication":"Nature Communications","title":"The effect of environmental information on evolution of cooperation in stochastic games","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","abstract":[{"text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.","lang":"eng"}],"intvolume":"        14","file":[{"file_id":"13337","date_updated":"2023-07-31T11:32:36Z","file_size":1601682,"checksum":"5aceefdfe76686267b93ae4fe81899f1","file_name":"2023_NatureComm_Kleshnina.pdf","relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2023-07-31T11:32:36Z","success":1}],"publication_status":"published","isi":1,"month":"07","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"pmid":1,"ddc":["000"],"day":"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"},"file_date_updated":"2023-07-31T11:32:36Z","article_number":"4153","scopus_import":"1","quality_controlled":"1","date_published":"2023-07-12T00:00:00Z","author":[{"last_name":"Kleshnina","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X"},{"first_name":"Stepan","last_name":"Simsa","orcid":"0000-0001-6687-1210","full_name":"Simsa, Stepan","id":"409d615c-2f95-11ee-b934-90a352102c1e"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"article_processing_charge":"Yes","doi":"10.1038/s41467-023-39625-9","date_updated":"2025-07-14T09:09:53Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"13336"}]}},{"has_accepted_license":"1","year":"2023","_id":"13260","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":15,"publication_identifier":{"eissn":["1759-6653"]},"citation":{"chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>.","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford Academic, 2023.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>."},"issue":"7","external_id":{"isi":["001023444700003"],"pmid":["37341535"]},"article_type":"original","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","status":"public","oa":1,"date_created":"2023-07-23T22:01:11Z","oa_version":"Published Version","publisher":"Oxford Academic","publication":"Genome biology and evolution","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","department":[{"_id":"BeVi"}],"abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"file":[{"file_id":"13339","date_updated":"2023-08-01T06:58:34Z","checksum":"70de3c4878de6efe00dc56de2df8812f","file_name":"2023_GBE_Barata.pdf","file_size":2382587,"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2023-08-01T06:58:34Z","success":1,"content_type":"application/pdf"}],"publication_status":"published","intvolume":"        15","isi":1,"month":"07","language":[{"iso":"eng"}],"ddc":["570"],"day":"01","pmid":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"},"article_number":"evad113","file_date_updated":"2023-08-01T06:58:34Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes","date_updated":"2023-08-02T06:42:35Z","doi":"10.1093/gbe/evad113","related_material":{"link":[{"relation":"software","url":"https://github.com/carolbarata/dpseudo-n-beyond"}]},"author":[{"id":"20565186-803f-11ed-ab7e-96a4ff7694ef","full_name":"De Castro Barbosa Rodrigues Barata, Carolina","last_name":"De Castro Barbosa Rodrigues Barata","first_name":"Carolina"},{"full_name":"Snook, Rhonda R.","first_name":"Rhonda R.","last_name":"Snook"},{"full_name":"Ritchie, Michael G.","last_name":"Ritchie","first_name":"Michael G."},{"full_name":"Kosiol, Carolin","first_name":"Carolin","last_name":"Kosiol"}],"date_published":"2023-07-01T00:00:00Z"},{"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"intvolume":"       380","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"343-2022"}],"language":[{"iso":"eng"}],"month":"06","isi":1,"day":"29","quality_controlled":"1","scopus_import":"1","date_updated":"2023-12-13T11:41:07Z","doi":"10.1126/science.adf5568","article_processing_charge":"No","author":[{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David"},{"full_name":"Chen, Hongtao","first_name":"Hongtao","last_name":"Chen"},{"full_name":"Barinov, Lev","first_name":"Lev","last_name":"Barinov"},{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"}],"date_published":"2023-06-29T00:00:00Z","year":"2023","_id":"13261","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1357-1362","volume":380,"publication_identifier":{"eissn":["1095-9203"]},"citation":{"apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>"},"external_id":{"isi":["001106405600028"]},"article_type":"original","issue":"6652","oa":1,"status":"public","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","oa_version":"Preprint","date_created":"2023-07-23T22:01:12Z","publisher":"American Association for the Advancement of Science","department":[{"_id":"EdHa"}],"title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","publication":"Science","abstract":[{"text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.","lang":"eng"}]},{"file_date_updated":"2023-07-31T10:53:08Z","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"},"conference":{"location":"Orlando, FL, United States","start_date":"2023-06-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2023-06-19"},"doi":"10.1145/3558481.3591082","date_updated":"2023-07-31T10:54:32Z","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov"},{"first_name":"Diba","last_name":"Hashemi","full_name":"Hashemi, Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783"},{"last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi"},{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-06-17T00:00:00Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2023-07-31T10:53:08Z","success":1,"date_updated":"2023-07-31T10:53:08Z","file_id":"13334","file_size":2087937,"checksum":"72e312aabf0c5248c99b5cd3a88e4c88","file_name":"2023_SPAA_Fedorov.pdf"}],"day":"17","ddc":["000"],"language":[{"iso":"eng"}],"month":"06","publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"title":"Provably-efficient and internally-deterministic parallel Union-Find","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","oa_version":"Published Version","date_created":"2023-07-23T22:01:12Z","arxiv":1,"abstract":[{"lang":"eng","text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited."}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"261-271","year":"2023","has_accepted_license":"1","_id":"13262","external_id":{"arxiv":["2304.09331"]},"status":"public","oa":1,"publication_identifier":{"isbn":["9781450395458"]},"citation":{"ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2023, pp. 261–71, doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271. doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL, United States, 2023, pp. 261–271.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 261–71. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>."}},{"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"language":[{"iso":"eng"}],"month":"06","isi":1,"day":"30","ddc":["000"],"pmid":1,"publication_status":"published","file":[{"content_type":"application/pdf","success":1,"date_created":"2023-07-31T11:09:05Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":641736,"file_name":"2023_Bioinformatics_Trinh.pdf","checksum":"ba3abe1171df1958413b7c7f957f5486","file_id":"13335","date_updated":"2023-07-31T11:09:05Z"}],"intvolume":"        39","quality_controlled":"1","scopus_import":"1","doi":"10.1093/bioinformatics/btad262","related_material":{"link":[{"url":"https://github.com/giang-trinh/trap-mvn","relation":"software"}]},"date_updated":"2023-12-13T11:41:52Z","article_processing_charge":"Yes","author":[{"full_name":"Trinh, Van Giang","first_name":"Van Giang","last_name":"Trinh"},{"first_name":"Belaid","last_name":"Benhamou","full_name":"Benhamou, Belaid"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"},{"orcid":"0000-0003-1993-0331","last_name":"Pastva","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel"}],"date_published":"2023-06-30T00:00:00Z","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"},"file_date_updated":"2023-07-31T11:09:05Z","publication_identifier":{"issn":["1367-4803"],"eissn":["1367-4811"]},"citation":{"ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522.","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>.","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.","ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>.","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>"},"external_id":{"isi":["001027457000060"],"pmid":["37387165"]},"article_type":"original","issue":"Supplement_1","status":"public","oa":1,"acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","has_accepted_license":"1","year":"2023","_id":"13263","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"i513-i522","volume":39,"abstract":[{"lang":"eng","text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models."}],"oa_version":"Published Version","ec_funded":1,"date_created":"2023-07-23T22:01:12Z","publisher":"Oxford Academic","department":[{"_id":"ToHe"}],"title":"Trap spaces of multi-valued networks: Definition, computation, and applications","publication":"Bioinformatics"},{"article_number":"064032","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"date_published":"2023-06-09T00:00:00Z","author":[{"full_name":"Phan, Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan"},{"full_name":"Falthansl-Scheinecker, Paul","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","first_name":"Paul","last_name":"Falthansl-Scheinecker"},{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","full_name":"Mishra, Umang","last_name":"Mishra","first_name":"Umang"},{"first_name":"W. M.","last_name":"Strickland","full_name":"Strickland, W. M."},{"full_name":"Langone, D.","last_name":"Langone","first_name":"D."},{"first_name":"J.","last_name":"Shabani","full_name":"Shabani, J."},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham"}],"related_material":{"record":[{"id":"14547","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-11-30T10:56:03Z","doi":"10.1103/PhysRevApplied.19.064032","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","intvolume":"        19","main_file_link":[{"url":"https://arxiv.org/abs/2206.05746","open_access":"1"}],"publication_status":"published","day":"09","language":[{"iso":"eng"}],"isi":1,"month":"06","title":"Gate-tunable superconductor-semiconductor parametric amplifier","department":[{"_id":"AnHi"},{"_id":"OnHo"}],"publication":"Physical Review Applied","publisher":"American Physical Society","oa_version":"Preprint","date_created":"2023-07-23T22:01:12Z","arxiv":1,"abstract":[{"lang":"eng","text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n"}],"volume":19,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13264","year":"2023","status":"public","oa":1,"acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","external_id":{"isi":["001012022600004"],"arxiv":["2206.05746"]},"article_type":"original","issue":"6","citation":{"ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>.","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>.","ieee":"D. T. Phan <i>et al.</i>, “Gate-tunable superconductor-semiconductor parametric amplifier,” <i>Physical Review Applied</i>, vol. 19, no. 6. American Physical Society, 2023.","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., &#38; Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>"},"publication_identifier":{"eissn":["2331-7019"]}},{"acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","status":"public","oa":1,"issue":"3","external_id":{"isi":["001018739600002"],"arxiv":["2201.02374"]},"article_type":"original","citation":{"apa":"Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>.","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3. Association for Computing Machinery, 2023.","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>.","ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>"},"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"volume":42,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"13265","year":"2023","arxiv":1,"abstract":[{"lang":"eng","text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality."}],"publication":"ACM Transactions on Graphics","department":[{"_id":"BeBi"}],"title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","publisher":"Association for Computing Machinery","date_created":"2023-07-23T22:01:13Z","oa_version":"Preprint","day":"17","month":"03","isi":1,"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.02374","open_access":"1"}],"intvolume":"        42","publication_status":"published","date_published":"2023-03-17T00:00:00Z","author":[{"first_name":"Fanchao","last_name":"Zhong","full_name":"Zhong, Fanchao"},{"full_name":"Xu, Yonglai","first_name":"Yonglai","last_name":"Xu"},{"id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","full_name":"Zhao, Haisen","last_name":"Zhao","orcid":"0000-0002-6389-1045","first_name":"Haisen"},{"full_name":"Lu, Lin","last_name":"Lu","first_name":"Lin"}],"article_processing_charge":"No","doi":"10.1145/3575859","date_updated":"2023-12-13T11:34:59Z","scopus_import":"1","quality_controlled":"1","article_number":"26"},{"_id":"13266","has_accepted_license":"1","year":"2023","volume":240,"page":"489-495","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>.","short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.","ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495.","ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. 2023;240(2):489-495. doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>","apa":"Qi, L., &#38; Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>.","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” <i>New Phytologist</i>, vol. 240, no. 2. Wiley, pp. 489–495, 2023."},"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"oa":1,"status":"public","acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","issue":"2","article_type":"original","external_id":{"pmid":["37434303"],"isi":["001026321500001"]},"date_created":"2023-07-23T22:01:13Z","oa_version":"Published Version","publication":"New Phytologist","title":"Tale of cAMP as a second messenger in auxin signaling and beyond","department":[{"_id":"JiFr"}],"publisher":"Wiley","abstract":[{"lang":"eng","text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general."}],"intvolume":"       240","file":[{"file_size":974464,"checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","file_name":"2023_NewPhytologist_Qi.pdf","date_updated":"2024-01-29T11:21:43Z","file_id":"14898","content_type":"application/pdf","date_created":"2024-01-29T11:21:43Z","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access"}],"publication_status":"published","isi":1,"month":"10","project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123","name":"Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"language":[{"iso":"eng"}],"pmid":1,"ddc":["580"],"day":"01","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"},"file_date_updated":"2024-01-29T11:21:43Z","scopus_import":"1","quality_controlled":"1","author":[{"last_name":"Qi","orcid":"0000-0001-5187-8401","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"date_published":"2023-10-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","doi":"10.1111/nph.19123","date_updated":"2024-01-29T11:21:55Z"},{"abstract":[{"lang":"eng","text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","publication":"Nature Methods","publisher":"Springer Nature","oa_version":"Published Version","ec_funded":1,"date_created":"2023-07-23T22:01:13Z","status":"public","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","oa":1,"article_type":"original","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"citation":{"ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>."},"publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"page":"1256-1265","volume":20,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13267","year":"2023","date_published":"2023-08-01T00:00:00Z","author":[{"full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky"},{"first_name":"Eder","orcid":"0000-0001-5665-0430","last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","full_name":"Michalska, Julia M","last_name":"Michalska","orcid":"0000-0003-3862-1235","first_name":"Julia M"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake"},{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr","first_name":"Wiebke"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","last_name":"Cenameri","first_name":"Alban"},{"full_name":"Broichhagen, Johannes","last_name":"Broichhagen","first_name":"Johannes"},{"last_name":"Grant","first_name":"Seth G.N.","full_name":"Grant, Seth G.N."},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"first_name":"Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G"}],"doi":"10.1038/s41592-023-01936-6","related_material":{"record":[{"id":"12817","status":"public","relation":"research_data"},{"id":"14770","relation":"shorter_version","status":"public"}],"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}]},"date_updated":"2024-01-10T08:37:48Z","article_processing_charge":"Yes","scopus_import":"1","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"pmid":1,"day":"01","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"},{"name":"The Wittgenstein 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The second author is supported by the Max Planck Institute for Mathematics and the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","publication_identifier":{"eissn":["1945-001X"],"issn":["1073-2780"]},"citation":{"short":"D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141.","mla":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>, vol. 30, no. 1, International Press, 2023, pp. 125–41, doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>.","ista":"Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141.","ama":"Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. 2023;30(1):125-141. doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>","apa":"Huybrechts, D., &#38; Mauri, M. (2023). On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. International Press. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>","chicago":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>. International Press, 2023. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>.","ieee":"D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,” <i>Mathematical Research Letters</i>, vol. 30, no. 1. International Press, pp. 125–141, 2023."},"publisher":"International Press","department":[{"_id":"TaHa"}],"title":"On type II degenerations of hyperkähler manifolds","publication":"Mathematical Research Letters","oa_version":"Preprint","date_created":"2023-07-23T22:01:14Z","ec_funded":1,"arxiv":1,"abstract":[{"text":"We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations.","lang":"eng"}],"publication_status":"published","intvolume":"        30","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.01587","open_access":"1"}],"day":"21","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"isi":1,"month":"06","doi":"10.4310/mrl.2023.v30.n1.a6","date_updated":"2024-01-16T12:00:47Z","article_processing_charge":"No","date_published":"2023-06-21T00:00:00Z","author":[{"last_name":"Huybrechts","first_name":"D.","full_name":"Huybrechts, D."},{"first_name":"Mirko","last_name":"Mauri","full_name":"Mauri, Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130"}],"quality_controlled":"1","scopus_import":"1"},{"abstract":[{"lang":"eng","text":"This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point."}],"arxiv":1,"date_created":"2023-07-23T22:01:14Z","oa_version":"Preprint","publication":"IEEE Transactions on Information Theory","department":[{"_id":"MaMo"}],"title":"Codes for the Z-channel","publisher":"Institute of Electrical and Electronics Engineers","citation":{"short":"N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357.","ista":"Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on Information Theory. 69(10), 6340–6357.","mla":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10, Institute of Electrical and Electronics Engineers, 2023, pp. 6340–57, doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>.","ama":"Polyanskii N, Zhang Y. Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. 2023;69(10):6340-6357. doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>","apa":"Polyanskii, N., &#38; Zhang, Y. (2023). Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>","chicago":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>.","ieee":"N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10. Institute of Electrical and Electronics Engineers, pp. 6340–6357, 2023."},"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"status":"public","oa":1,"acknowledgement":"Nikita Polyanskii’s research was conducted in part during October 2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute of Science and Technology. His work was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang is supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","issue":"10","external_id":{"arxiv":["2105.01427"],"isi":["001069680100011"]},"article_type":"original","_id":"13269","year":"2023","volume":69,"page":"6340-6357","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Polyanskii, Nikita","first_name":"Nikita","last_name":"Polyanskii"},{"id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","last_name":"Zhang","orcid":"0000-0002-6465-6258","first_name":"Yihan"}],"date_published":"2023-07-04T00:00:00Z","article_processing_charge":"No","doi":"10.1109/TIT.2023.3292219","date_updated":"2024-01-29T11:10:54Z","isi":1,"month":"07","language":[{"iso":"eng"}],"day":"04","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.01427","open_access":"1"}],"intvolume":"        69","publication_status":"published"},{"date_created":"2023-07-23T22:01:14Z","oa_version":"Published Version","publisher":"Springer Nature","publication":"Discrete and Computational Geometry","title":"Iterated medial triangle subdivision in surfaces of constant curvature","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0\r\n such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses."}],"arxiv":1,"year":"2023","has_accepted_license":"1","_id":"13270","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":70,"page":"1059-1089","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"citation":{"apa":"Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>","ieee":"F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant curvature,” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3. Springer Nature, pp. 1059–1089, 2023.","chicago":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>.","ista":"Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089.","short":"F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089.","mla":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3, Springer Nature, 2023, pp. 1059–89, doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>.","ama":"Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. 2023;70(3):1059-1089. doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>"},"issue":"3","article_type":"original","external_id":{"arxiv":["2107.04112"],"isi":["001023742800003"]},"oa":1,"status":"public","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","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"},"file_date_updated":"2024-01-29T11:15:22Z","quality_controlled":"1","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00454-023-00500-5","date_updated":"2024-01-29T11:16:16Z","author":[{"last_name":"Brunck","first_name":"Florestan R","id":"6ab6e556-f394-11eb-9cf6-9dfb78f00d8d","full_name":"Brunck, Florestan R"}],"date_published":"2023-07-05T00:00:00Z","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2024-01-29T11:15:22Z","date_updated":"2024-01-29T11:15:22Z","file_id":"14897","file_size":1466020,"file_name":"2023_DiscreteComputGeometry_Brunck.pdf","checksum":"865e68daafdd4edcfc280172ec50f5ea"}],"publication_status":"published","intvolume":"        70","isi":1,"month":"07","language":[{"iso":"eng"}],"ddc":["510"],"day":"05"},{"day":"08","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis","grant_number":"M03337"}],"language":[{"iso":"eng"}],"isi":1,"month":"07","publication_status":"epub_ahead","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.05785"}],"doi":"10.1007/s00023-023-01345-7","date_updated":"2023-12-13T11:33:46Z","article_processing_charge":"No","date_published":"2023-07-08T00:00:00Z","author":[{"first_name":"Haonan","last_name":"Zhang","full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"quality_controlled":"1","scopus_import":"1","article_type":"original","external_id":{"isi":["001025709100001"],"arxiv":["2108.05785"]},"oa":1,"acknowledgement":"I am grateful to Boguslaw Zegarliński for asking me the questions in [3] and for helpful communication. I also want to thank Paata Ivanisvili for drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous referee for the valuable comments and for pointing out some errors in an earlier version of the paper. This work is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337.","status":"public","publication_identifier":{"issn":["1424-0637"]},"citation":{"short":"H. Zhang, Annales Henri Poincare (2023).","ista":"Zhang H. 2023. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare.","mla":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” <i>Annales Henri Poincare</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00023-023-01345-7\">10.1007/s00023-023-01345-7</a>.","ama":"Zhang H. Some convexity and monotonicity results of trace functionals. <i>Annales Henri Poincare</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s00023-023-01345-7\">10.1007/s00023-023-01345-7</a>","apa":"Zhang, H. (2023). Some convexity and monotonicity results of trace functionals. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-023-01345-7\">https://doi.org/10.1007/s00023-023-01345-7</a>","chicago":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-023-01345-7\">https://doi.org/10.1007/s00023-023-01345-7</a>.","ieee":"H. Zhang, “Some convexity and monotonicity results of trace functionals,” <i>Annales Henri Poincare</i>. Springer Nature, 2023."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","_id":"13271","arxiv":1,"abstract":[{"text":"In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems.","lang":"eng"}],"publisher":"Springer Nature","department":[{"_id":"JaMa"}],"title":"Some convexity and monotonicity results of trace functionals","publication":"Annales Henri Poincare","oa_version":"Preprint","ec_funded":1,"date_created":"2023-07-23T22:01:15Z"},{"isi":1,"month":"07","language":[{"iso":"eng"}],"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"day":"21","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05098","open_access":"1"}],"intvolume":"       131","quality_controlled":"1","keyword":["General Physics and Astronomy"],"article_processing_charge":"No","doi":"10.1103/physrevlett.131.034002","date_updated":"2023-12-13T11:40:19Z","date_published":"2023-07-21T00:00:00Z","author":[{"last_name":"Paranjape","first_name":"Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","full_name":"Paranjape, Chaitanya S"},{"full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz"},{"full_name":"Duguet, Yohann","first_name":"Yohann","last_name":"Duguet"},{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"article_number":"034002","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"citation":{"chicago":"Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.131.034002\">https://doi.org/10.1103/physrevlett.131.034002</a>.","ieee":"C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” <i>Physical Review Letters</i>, vol. 131, no. 3. American Physical Society, 2023.","apa":"Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., &#38; Hof, B. (2023). Direct path from turbulence to time-periodic solutions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.131.034002\">https://doi.org/10.1103/physrevlett.131.034002</a>","ama":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. <i>Physical Review Letters</i>. 2023;131(3). doi:<a href=\"https://doi.org/10.1103/physrevlett.131.034002\">10.1103/physrevlett.131.034002</a>","mla":"Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” <i>Physical Review Letters</i>, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.131.034002\">10.1103/physrevlett.131.034002</a>.","ista":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.","short":"C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023)."},"issue":"3","external_id":{"isi":["001052929900004"],"arxiv":["2306.05098"]},"article_type":"original","status":"public","oa":1,"acknowledgement":"We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.).","year":"2023","_id":"13274","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":131,"abstract":[{"lang":"eng","text":"Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics."}],"arxiv":1,"date_created":"2023-07-24T09:43:59Z","oa_version":"Preprint","publisher":"American Physical Society","publication":"Physical Review Letters","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"title":"Direct path from turbulence to time-periodic solutions"},{"publisher":"SciPost Foundation","title":"Codebase release 1.0 for FermiFCI","department":[{"_id":"MiLe"}],"ec_funded":1,"date_created":"2023-07-24T10:46:23Z","oa_version":"Published Version","article_processing_charge":"No","related_material":{"record":[{"id":"13276","status":"public","relation":"used_in_publication"}]},"doi":"10.21468/scipostphyscodeb.12-r1.0","date_updated":"2023-07-31T09:16:02Z","date_published":"2023-04-19T00:00:00Z","author":[{"full_name":"Rammelmüller, Lukas","first_name":"Lukas","last_name":"Rammelmüller"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","year":"2023","_id":"13275","main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"ddc":["530"],"day":"19","oa":1,"status":"public","month":"04","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"citation":{"chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>.","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>","mla":"Rammelmüller, Lukas, et al. <i>Codebase Release 1.0 for FermiFCI</i>. SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>."}},{"article_number":"12","file_date_updated":"2023-07-31T09:09:23Z","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"},"related_material":{"record":[{"id":"13275","relation":"research_data","status":"public"}]},"date_updated":"2023-07-31T09:16:02Z","doi":"10.21468/scipostphyscodeb.12","article_processing_charge":"No","date_published":"2023-04-19T00:00:00Z","author":[{"full_name":"Rammelmüller, Lukas","first_name":"Lukas","last_name":"Rammelmüller"},{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-07-31T09:09:23Z","success":1,"file_id":"13330","date_updated":"2023-07-31T09:09:23Z","file_size":551418,"checksum":"f583a70fe915d2208c803f5afb426daa","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf"}],"day":"19","ddc":["530"],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"04","publisher":"SciPost Foundation","title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","department":[{"_id":"MiLe"}],"publication":"SciPost Physics Codebases","oa_version":"Published Version","ec_funded":1,"date_created":"2023-07-24T10:47:15Z","arxiv":1,"abstract":[{"text":"<jats:p>We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.</jats:p>","lang":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","year":"2023","_id":"13276","article_type":"original","external_id":{"arxiv":["2202.04603"]},"oa":1,"acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","status":"public","publication_identifier":{"issn":["2949-804X"]},"citation":{"apa":"Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics Codebases</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">https://doi.org/10.21468/scipostphyscodeb.12</a>","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">https://doi.org/10.21468/scipostphyscodeb.12</a>.","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023.","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” <i>SciPost Physics Codebases</i>, 12, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">10.21468/scipostphyscodeb.12</a>.","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics Codebases</i>. 2023. doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">10.21468/scipostphyscodeb.12</a>"}}]