[{"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer Nature","ddc":["510"],"year":"2021","article_number":"4009","date_published":"2021-06-29T00:00:00Z","pmid":1,"article_processing_charge":"No","intvolume":"        12","volume":12,"external_id":{"pmid":["34188036"],"isi":["000671752100003"]},"_id":"9640","issue":"1","author":[{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"isi":1,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"2021_NatCoom_Tkadlec.pdf","file_id":"9692","date_created":"2021-07-19T13:02:20Z","creator":"cziletti","file_size":628992,"date_updated":"2021-07-19T13:02:20Z","access_level":"open_access","success":1,"checksum":"5767418926a7f7fb76151de29473dae0","relation":"main_file","content_type":"application/pdf"}],"citation":{"chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>.","mla":"Tkadlec, Josef, et al. “Fast and Strong Amplifiers of Natural Selection.” <i>Nature Communications</i>, vol. 12, no. 1, 4009, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Nature Communications 12 (2021).","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2021. Fast and strong amplifiers of natural selection. Nature Communications. 12(1), 4009.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Fast and strong amplifiers of natural selection,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-24271-w\">10.1038/s41467-021-24271-w</a>","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2021). Fast and strong amplifiers of natural selection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-24271-w\">https://doi.org/10.1038/s41467-021-24271-w</a>"},"scopus_import":"1","acknowledgement":"K.C. acknowledges support from ERC Start grant no. (279307: Graph Games), ERC Consolidator grant no. (863818: ForM-SMart), Austrian Science Fund (FWF) grant no. P23499-N23 and S11407-N23 (RiSE). M.A.N. acknowledges support from Office of Naval Research grant N00014-16-1-2914 and from the John Templeton Foundation.","month":"06","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"doi":"10.1038/s41467-021-24271-w","day":"29","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed."}],"publication":"Nature Communications","date_created":"2021-07-11T22:01:15Z","publication_identifier":{"eissn":["2041-1723"]},"file_date_updated":"2021-07-19T13:02:20Z","type":"journal_article","date_updated":"2026-04-02T14:04:10Z","article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Fast and strong amplifiers of natural selection","has_accepted_license":"1","oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The role of hippocampal mossy cells in novelty detection","article_type":"original","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["1074-7427"],"eissn":["1095-9564"]},"publication":"Neurobiology of Learning and Memory","date_created":"2021-07-11T22:01:16Z","abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}],"date_updated":"2025-07-10T12:02:00Z","type":"journal_article","file_date_updated":"2021-07-19T13:46:06Z","doi":"10.1016/j.nlm.2021.107486","day":"30","ec_funded":1,"department":[{"_id":"RySh"}],"publication_status":"published","month":"06","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","citation":{"ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>.","mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>, vol. 183, 107486, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>.","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. 2021;183. doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>","apa":"Fredes, F., &#38; Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” <i>Neurobiology of Learning and Memory</i>, vol. 183. Elsevier, 2021."},"file":[{"relation":"main_file","checksum":"8e8298a9e8c7df146ad23f32c2a63929","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":1994793,"creator":"cziletti","date_updated":"2021-07-19T13:46:06Z","file_name":"2021_NeurobLearnMemory_Fredes.pdf","file_id":"9694","date_created":"2021-07-19T13:46:06Z"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","scopus_import":"1","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","_id":"9641","external_id":{"isi":["000677694900004"],"pmid":["34214666"]},"author":[{"last_name":"Fredes","full_name":"Fredes, Felipe","first_name":"Felipe"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"}],"isi":1,"intvolume":"       183","volume":183,"date_published":"2021-06-30T00:00:00Z","pmid":1,"article_processing_charge":"No","ddc":["610"],"publisher":"Elsevier","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour"}],"article_number":"107486","year":"2021"},{"oa":1,"has_accepted_license":"1","article_type":"original","title":"Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2021-07-19T13:32:17Z","type":"journal_article","date_updated":"2026-04-03T09:46:05Z","abstract":[{"text":"Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain.","lang":"eng"}],"publication":"Cell Reports","date_created":"2021-07-11T22:01:16Z","publication_identifier":{"eissn":["2211-1247"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-twinkle-and-the-brain/","relation":"press_release"}]},"month":"07","department":[{"_id":"SaSi"}],"publication_status":"published","doi":"10.1016/j.celrep.2021.109313","ec_funded":1,"day":"06","scopus_import":"1","acknowledgement":"We thank the scientific service units at IST Austria, especially the IST bioimaging facility, the preclinical facility, and, specifically, Michael Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King, and all Siegert group members for constant feedback on the project and manuscript; Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination for OD plasticity experiments; and Ana Morello from MIT for technical assistance with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian Academy of Sciences at the Institute of Science and Technology Austria to R.S., from the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the European Research Council (grant 715571 to S.S.), and the National Eye Institute of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.) and R01EY023037 (diversity supplement to H.D.J-C.).","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. 2021;36(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>","apa":"Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar, F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>","ieee":"A. Venturino <i>et al.</i>, “Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,” <i>Cell Reports</i>, vol. 36, no. 1. Elsevier, 2021.","ista":"Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar F, Colombo G, Cubero RJ, Miteva FE, Bear MF, Siegert S. 2021. Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.","short":"A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar, G. Colombo, R.J. Cubero, F.E. Miteva, M.F. Bear, S. Siegert, Cell Reports 36 (2021).","mla":"Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>, vol. 36, no. 1, 109313, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">10.1016/j.celrep.2021.109313</a>.","chicago":"Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109313\">https://doi.org/10.1016/j.celrep.2021.109313</a>."},"file":[{"access_level":"open_access","success":1,"checksum":"f056255f6d01fd9a86b5387635928173","relation":"main_file","content_type":"application/pdf","file_name":"2021_CellReports_Venturino.pdf","file_id":"9693","date_created":"2021-07-19T13:32:17Z","creator":"cziletti","file_size":56388540,"date_updated":"2021-07-19T13:32:17Z"}],"isi":1,"author":[{"last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","first_name":"Alessandro","orcid":"0000-0003-2356-9403"},{"orcid":"0000-0001-5297-733X","first_name":"Rouven","last_name":"Schulz","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Héctor","last_name":"De Jesús-Cortés","full_name":"De Jesús-Cortés, Héctor"},{"first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","last_name":"Maes"},{"id":"93C65ECC-A6F2-11E9-8DF9-9712E6697425","full_name":"Nagy, Balint","last_name":"Nagy","first_name":"Balint"},{"first_name":"Francis","last_name":"Reilly-Andújar","full_name":"Reilly-Andújar, Francis"},{"id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","full_name":"Colombo, Gloria","last_name":"Colombo","first_name":"Gloria","orcid":"0000-0001-9434-8902"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","full_name":"Cubero, Ryan J","last_name":"Cubero","first_name":"Ryan J","orcid":"0000-0003-0002-1867"},{"first_name":"Florianne E","last_name":"Schoot Uiterkamp","full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark F.","full_name":"Bear, Mark F.","last_name":"Bear"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"}],"issue":"1","_id":"9642","external_id":{"pmid":["34233180"],"isi":["000670188500004"]},"volume":36,"intvolume":"        36","article_processing_charge":"No","pmid":1,"date_published":"2021-07-06T00:00:00Z","year":"2021","article_number":"109313","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"publisher":"Elsevier","ddc":["570"]},{"isi":1,"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Goharshady","full_name":"Goharshady, Ehsan Kafshdar","first_name":"Ehsan Kafshdar"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr"},{"orcid":"0000-0002-4681-1699","first_name":"Dorde","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic"}],"external_id":{"isi":["000723661700067"],"arxiv":["2104.01189"]},"_id":"9644","page":"1033-1048","article_processing_charge":"No","date_published":"2021-06-01T00:00:00Z","year":"2021","publisher":"Association for Computing Machinery","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"conference":{"location":"Online","end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20"},"title":"Proving non-termination by program reversal","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2026-04-07T13:27:55Z","type":"conference","publication_identifier":{"isbn":["9781450383912"]},"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","date_created":"2021-07-11T22:01:17Z","abstract":[{"text":"We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.","lang":"eng"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","arxiv":1,"doi":"10.1145/3453483.3454093","day":"01","ec_funded":1,"department":[{"_id":"KrCh"}],"publication_status":"published","month":"06","related_material":{"record":[{"status":"public","relation":"research_data","id":"15284"},{"id":"14539","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech Science Foundation grant No. GJ19-15134Y.","citation":{"ama":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination by program reversal. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1033-1048. doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., &#38; Zikelic, D. (2021). Proving non-termination by program reversal. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1033–1048). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination by program reversal,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1033–1048.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1033–1048.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde Zikelic. “Proving Non-Termination by Program Reversal.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1033–48. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454093\">https://doi.org/10.1145/3453483.3454093</a>.","mla":"Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1033–48, doi:<a href=\"https://doi.org/10.1145/3453483.3454093\">10.1145/3453483.3454093</a>.","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.01189"}],"status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Polynomial reachability witnesses via Stellensätze","conference":{"end_date":"2021-06-26","location":"Online","start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation"},"oa":1,"abstract":[{"text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.","lang":"eng"}],"publication_identifier":{"isbn":["9781450383912"]},"date_created":"2021-07-11T22:01:17Z","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","date_updated":"2025-07-10T12:02:00Z","type":"conference","month":"06","doi":"10.1145/3453483.3454076","day":"01","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Submitted Version","status":"public","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03183862/"}],"citation":{"ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 772–787.","ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:772-787. doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., &#38; Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 772–787). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787.","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 772–87. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>.","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 772–87, doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>.","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787."},"scopus_import":"1","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","external_id":{"isi":["000723661700050"]},"_id":"9645","isi":1,"author":[{"last_name":"Asadi","full_name":"Asadi, Ali","first_name":"Ali"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Hongfei","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar"},{"first_name":"Mohammad","last_name":"Mahdavi","full_name":"Mahdavi, Mohammad"}],"date_published":"2021-06-01T00:00:00Z","article_processing_charge":"No","page":"772-787","publisher":"Association for Computing Machinery","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"year":"2021"},{"page":"1171-1186","article_processing_charge":"No","date_published":"2021-06-01T00:00:00Z","year":"2021","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"publisher":"Association for Computing Machinery","isi":1,"author":[{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"first_name":"Yican","full_name":"Sun, Yican","last_name":"Sun"},{"first_name":"Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584"}],"_id":"9646","external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","arxiv":1,"department":[{"_id":"KrCh"}],"publication_status":"published","day":"01","ec_funded":1,"doi":"10.1145/3453483.3454102","month":"06","scopus_import":"1","acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","citation":{"ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1171–86, doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1171–86. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1171-1186. doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1171–1186). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1171–1186."},"main_file_link":[{"url":"https://arxiv.org/abs/2011.14617","open_access":"1"}],"status":"public","oa":1,"conference":{"location":"Online","end_date":"2021-06-26","name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Quantitative analysis of assertion violations in probabilistic programs","type":"conference","date_updated":"2025-04-15T07:55:05Z","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","date_created":"2021-07-11T22:01:18Z","publication_identifier":{"isbn":["9781450383912"]},"abstract":[{"lang":"eng","text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude."}]},{"ddc":["004"],"project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publisher":"Elsevier","year":"2021","date_published":"2021-06-04T00:00:00Z","page":"1-16","article_processing_charge":"No","intvolume":"       893","volume":893,"external_id":{"isi":["000710180500002"]},"_id":"9647","author":[{"first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana"},{"last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"d3aef34cfb13e53bba4cf44d01680793","relation":"main_file","date_created":"2022-05-12T12:13:27Z","file_id":"11364","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_updated":"2022-05-12T12:13:27Z","creator":"dernst","file_size":2566504}],"citation":{"ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>, vol. 893, Elsevier, 2021, pp. 1–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>.","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. 2021;893:1-16. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., &#38; Guet, C. C. (2021). Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” <i>Theoretical Computer Science</i>, vol. 893. Elsevier, pp. 1–16, 2021."},"status":"public","scopus_import":"1","acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"doi":"10.1016/j.tcs.2021.05.023","day":"04","corr_author":"1","month":"06","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Theoretical Computer Science","date_created":"2021-07-11T22:01:18Z","publication_identifier":{"issn":["0304-3975"]},"abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"type":"journal_article","date_updated":"2025-04-15T06:25:56Z","file_date_updated":"2022-05-12T12:13:27Z","title":"Long lived transients in gene regulation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","has_accepted_license":"1","oa":1},{"corr_author":"1","month":"10","publication_status":"published","department":[{"_id":"JiFr"}],"doi":"10.1111/nph.17617","ec_funded":1,"day":"01","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"date_updated":"2021-10-07T13:42:47Z","file_size":1939800,"creator":"kschuh","date_created":"2021-10-07T13:42:47Z","file_id":"10105","file_name":"2021_NewPhytologist_Han.pdf","content_type":"application/pdf","relation":"main_file","checksum":"6422a6eb329b52d96279daaee0fcf189","success":1,"access_level":"open_access"}],"citation":{"ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522."},"scopus_import":"1","acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","has_accepted_license":"1","oa":1,"abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"date_created":"2021-07-14T15:29:14Z","publication":"New Phytologist","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"file_date_updated":"2021-10-07T13:42:47Z","type":"journal_article","date_updated":"2025-04-14T07:45:00Z","pmid":1,"date_published":"2021-10-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","page":"510-522","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publisher":"Wiley","ddc":["580"],"year":"2021","issue":"2","_id":"9656","external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"isi":1,"author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"},{"orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5187-8401","first_name":"Linlin","last_name":"Qi","full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"first_name":"SS","last_name":"Alotaibi","full_name":"Alotaibi, SS"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"intvolume":"       232","volume":232},{"author":[{"last_name":"Gao","full_name":"Gao, Z","first_name":"Z"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"full_name":"Ke, M","last_name":"Ke","first_name":"M"},{"first_name":"H","last_name":"Xu","full_name":"Xu, H"},{"last_name":"Xu","full_name":"Xu, Q","first_name":"Q"},{"first_name":"J","full_name":"Chen, J","last_name":"Chen"},{"last_name":"Li","full_name":"Li, Y","first_name":"Y"},{"first_name":"L","full_name":"Huang, L","last_name":"Huang"},{"last_name":"Zhao","full_name":"Zhao, H","first_name":"H"},{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"first_name":"S","full_name":"Mai, S","last_name":"Mai"},{"first_name":"T","last_name":"Xu","full_name":"Xu, T"},{"last_name":"Liu","full_name":"Liu, X","first_name":"X"},{"last_name":"Li","full_name":"Li, S","first_name":"S"},{"first_name":"Y","last_name":"Guan","full_name":"Guan, Y"},{"last_name":"Yang","full_name":"Yang, W","first_name":"W"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"J","full_name":"Petrášek, J","last_name":"Petrášek"},{"first_name":"J","last_name":"Zhang","full_name":"Zhang, J"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"}],"isi":1,"external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"_id":"9657","issue":"9","volume":33,"intvolume":"        33","article_processing_charge":"No","page":"2981–3003","date_published":"2021-07-07T00:00:00Z","pmid":1,"year":"2021","publisher":"American Society of Plant Biologists","ddc":["580"],"oa":1,"has_accepted_license":"1","article_type":"original","title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-07-19T12:13:34Z","type":"journal_article","date_updated":"2024-10-21T06:02:03Z","abstract":[{"text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.","lang":"eng"}],"publication":"Plant Cell","date_created":"2021-07-14T15:32:43Z","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"07","department":[{"_id":"JiFr"}],"publication_status":"published","day":"07","doi":"10.1093/plcell/koab183","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>."},"file":[{"success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"6715712ec306c321f0204c817b7f8ae7","file_id":"9691","date_created":"2021-07-19T12:13:34Z","file_name":"2021_PlantCell_Gao.pdf","date_updated":"2021-07-19T12:13:34Z","file_size":10566921,"creator":"cziletti"}]},{"article_processing_charge":"No","date_published":"2021-01-26T00:00:00Z","pmid":1,"year":"2021","article_number":"588","publisher":"Springer Nature","ddc":["530","540"],"author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"_id":"9669","issue":"1","external_id":{"arxiv":["2010.13729"],"pmid":["33500405"]},"extern":"1","volume":12,"intvolume":"        12","arxiv":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","month":"01","publication_status":"published","day":"26","doi":"10.1038/s41467-020-20821-w","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"short":"A. Reinhardt, B. Cheng, Nature Communications 12 (2021).","mla":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” <i>Nature Communications</i>, vol. 12, no. 1, 588, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-020-20821-w\">10.1038/s41467-020-20821-w</a>.","chicago":"Reinhardt, Aleks, and Bingqing Cheng. “Quantum-Mechanical Exploration of the Phase Diagram of Water.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-020-20821-w\">https://doi.org/10.1038/s41467-020-20821-w</a>.","ista":"Reinhardt A, Cheng B. 2021. Quantum-mechanical exploration of the phase diagram of water. Nature Communications. 12(1), 588.","ieee":"A. Reinhardt and B. Cheng, “Quantum-mechanical exploration of the phase diagram of water,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","apa":"Reinhardt, A., &#38; Cheng, B. (2021). Quantum-mechanical exploration of the phase diagram of water. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20821-w\">https://doi.org/10.1038/s41467-020-20821-w</a>","ama":"Reinhardt A, Cheng B. Quantum-mechanical exploration of the phase diagram of water. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-20821-w\">10.1038/s41467-020-20821-w</a>"},"file":[{"success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"8b5e1fbe2f1ab936047008043150e894","date_created":"2021-07-15T13:55:46Z","file_id":"9670","file_name":"2021_NatureCommunications_Reinhardt.pdf","date_updated":"2021-07-15T13:55:46Z","file_size":1180227,"creator":"asandaue"}],"has_accepted_license":"1","oa":1,"article_type":"original","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Quantum-mechanical exploration of the phase diagram of water","file_date_updated":"2021-07-15T13:55:46Z","type":"journal_article","date_updated":"2023-02-23T14:04:20Z","abstract":[{"lang":"eng","text":"The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations."}],"publication":"Nature Communications","date_created":"2021-07-15T13:48:13Z","publication_identifier":{"eissn":["2041-1723"]}},{"date_published":"2021-07-06T00:00:00Z","page":"129-139","article_processing_charge":"No","project":[{"grant_number":"840605","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"year":"2021","_id":"9678","external_id":{"arxiv":["2005.07761"]},"author":[{"first_name":"Sebastian","full_name":"Brandt, Sebastian","last_name":"Brandt"},{"full_name":"Keller, Barbara","last_name":"Keller","first_name":"Barbara"},{"first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","last_name":"Rybicki"},{"full_name":"Suomela, Jukka","last_name":"Suomela","first_name":"Jukka"},{"full_name":"Uitto, Jara","last_name":"Uitto","first_name":"Jara"}],"ec_funded":1,"doi":"10.1145/3409964.3461785","day":"06","department":[{"_id":"DaAl"}],"publication_status":"published","month":"07","related_material":{"record":[{"id":"15074","relation":"earlier_version","status":"public"}]},"oa_version":"Preprint","quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"citation":{"short":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.","mla":"Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token Dropping.” <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 2021, pp. 129–39, doi:<a href=\"https://doi.org/10.1145/3409964.3461785\">10.1145/3409964.3461785</a>.","chicago":"Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>, 129–39, 2021. <a href=\"https://doi.org/10.1145/3409964.3461785\">https://doi.org/10.1145/3409964.3461785</a>.","ista":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures , 129–139.","ieee":"S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing through distributed token dropping,” in <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>,  Virtual Event, United States, 2021, pp. 129–139.","ama":"Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing through distributed token dropping. In: <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i>. ; 2021:129-139. doi:<a href=\"https://doi.org/10.1145/3409964.3461785\">10.1145/3409964.3461785</a>","apa":"Brandt, S., Keller, B., Rybicki, J., Suomela, J., &#38; Uitto, J. (2021). Efficient load-balancing through distributed token dropping. In <i>Annual ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 129–139).  Virtual Event, United States. <a href=\"https://doi.org/10.1145/3409964.3461785\">https://doi.org/10.1145/3409964.3461785</a>"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.07761"}],"status":"public","scopus_import":"1","acknowledgement":"We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable discussions. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 840605.","title":"Efficient load-balancing through distributed token dropping","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"conference":{"start_date":"2021-07-06","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures ","end_date":"2021-07-08","location":" Virtual Event, United States"},"publication_identifier":{"isbn":["9781450380706"]},"date_created":"2021-07-18T22:01:22Z","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","abstract":[{"text":"We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.","lang":"eng"}],"date_updated":"2025-04-14T07:50:55Z","type":"conference"},{"ddc":["530"],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"IOP Publishing","year":"2021","article_number":"065009","date_published":"2021-06-23T00:00:00Z","article_processing_charge":"Yes","intvolume":"        23","volume":23,"_id":"9679","external_id":{"isi":["000664736300001"],"arxiv":["2102.04961"]},"issue":"6","isi":1,"author":[{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"full_name":"Marchukov, Oleksandr V.","last_name":"Marchukov","first_name":"Oleksandr V."},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"checksum":"e39164ce7ea228d287cf8924e1a0f9fe","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"cziletti","file_size":3868445,"date_updated":"2021-07-19T11:47:16Z","file_name":"2021_NewJPhys_Huber.pdf","file_id":"9690","date_created":"2021-07-19T11:47:16Z"}],"citation":{"ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>.","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009."},"status":"public","scopus_import":"1","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","publication_status":"published","department":[{"_id":"MiLe"}],"ec_funded":1,"doi":"10.1088/1367-2630/ac0576","day":"23","month":"06","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"date_created":"2021-07-18T22:01:22Z","publication":"New Journal of Physics","publication_identifier":{"eissn":["1367-2630"]},"abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"type":"journal_article","date_updated":"2026-04-02T14:01:49Z","file_date_updated":"2021-07-19T11:47:16Z","title":"Morphology of three-body quantum states from machine learning","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","oa":1,"has_accepted_license":"1"},{"arxiv":1,"article_processing_charge":"No","oa_version":"Preprint","language":[{"iso":"eng"}],"date_published":"2021-03-16T00:00:00Z","month":"03","related_material":{"record":[{"status":"public","relation":"later_version","id":"19909"}]},"doi":"10.48550/arXiv.2103.09035","day":"16","publication_status":"submitted","article_number":"2103.09035","year":"2021","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.09035"}],"citation":{"apa":"Cheng, B., Bethkenhagen, M., Pickard, C. J., &#38; Hamel, S. (n.d.). Predicting the phase behaviors of superionic water at planetary conditions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2103.09035\">https://doi.org/10.48550/arXiv.2103.09035</a>","ama":"Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors of superionic water at planetary conditions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2103.09035\">10.48550/arXiv.2103.09035</a>","ieee":"B. Cheng, M. Bethkenhagen, C. J. Pickard, and S. Hamel, “Predicting the phase behaviors of superionic water at planetary conditions,” <i>arXiv</i>. .","ista":"Cheng B, Bethkenhagen M, Pickard CJ, Hamel S. Predicting the phase behaviors of superionic water at planetary conditions. arXiv, 2103.09035.","mla":"Cheng, Bingqing, et al. “Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.” <i>ArXiv</i>, 2103.09035, doi:<a href=\"https://doi.org/10.48550/arXiv.2103.09035\">10.48550/arXiv.2103.09035</a>.","chicago":"Cheng, Bingqing, Mandy Bethkenhagen, Chris J. Pickard, and Sebastien Hamel. “Predicting the Phase Behaviors of Superionic Water at Planetary Conditions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2103.09035\">https://doi.org/10.48550/arXiv.2103.09035</a>.","short":"B. Cheng, M. Bethkenhagen, C.J. Pickard, S. Hamel, ArXiv (n.d.)."},"author":[{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng"},{"full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen","first_name":"Mandy"},{"first_name":"Chris J.","full_name":"Pickard, Chris J.","last_name":"Pickard"},{"last_name":"Hamel","full_name":"Hamel, Sebastien","first_name":"Sebastien"}],"oa":1,"_id":"9696","external_id":{"arxiv":["2103.09035"]},"extern":"1","title":"Predicting the phase behaviors of superionic water at planetary conditions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-26T11:49:07Z","type":"preprint","abstract":[{"text":"Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to overcome the limitations of quantum mechanical simulations, and characterize hydrogen diffusion, superionic transitions, and phase behaviors of water at extreme conditions. We predict that a close-packed superionic phase with mixed stacking is stable over a wide temperature and pressure range, while a body-centered cubic phase is only thermodynamically stable in a small window but is kinetically favored. Our phase boundaries, which are consistent with the existing-albeit scarce-experimental observations, help resolve the fractions of insulating ice, different superionic phases, and liquid water inside of ice giants.","lang":"eng"}],"publication":"arXiv","date_created":"2021-07-20T06:42:29Z"},{"date_published":"2021-07-07T00:00:00Z","page":"9816-9872","article_processing_charge":"No","publisher":"American Chemical Society","year":"2021","external_id":{"arxiv":["2102.06321"]},"_id":"9698","extern":"1","issue":"16","author":[{"first_name":"John A.","full_name":"Keith, John A.","last_name":"Keith"},{"first_name":"Valentin","full_name":"Valentin Vassilev-Galindo, Valentin","last_name":"Valentin Vassilev-Galindo"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632"},{"full_name":"Chmiela, Stefan","last_name":"Chmiela","first_name":"Stefan"},{"last_name":"Gastegger","full_name":"Gastegger, Michael","first_name":"Michael"},{"first_name":"Klaus-Robert","last_name":"Müller","full_name":"Müller, Klaus-Robert"},{"last_name":"Tkatchenko","full_name":"Tkatchenko, Alexandre","first_name":"Alexandre"}],"intvolume":"       121","volume":121,"doi":"10.1021/acs.chemrev.1c00107","day":"07","publication_status":"published","month":"07","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"citation":{"chicago":"Keith, John A., Valentin Valentin Vassilev-Galindo, Bingqing Cheng, Stefan Chmiela, Michael Gastegger, Klaus-Robert Müller, and Alexandre Tkatchenko. “Combining Machine Learning and Computational Chemistry for Predictive Insights into Chemical Systems.” <i>Chemical Reviews</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">https://doi.org/10.1021/acs.chemrev.1c00107</a>.","short":"J.A. Keith, V. Valentin Vassilev-Galindo, B. Cheng, S. Chmiela, M. Gastegger, K.-R. Müller, A. Tkatchenko, Chemical Reviews 121 (2021) 9816–9872.","mla":"Keith, John A., et al. “Combining Machine Learning and Computational Chemistry for Predictive Insights into Chemical Systems.” <i>Chemical Reviews</i>, vol. 121, no. 16, American Chemical Society, 2021, pp. 9816–72, doi:<a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">10.1021/acs.chemrev.1c00107</a>.","ista":"Keith JA, Valentin Vassilev-Galindo V, Cheng B, Chmiela S, Gastegger M, Müller K-R, Tkatchenko A. 2021. Combining machine learning and computational chemistry for predictive insights into chemical systems. Chemical Reviews. 121(16), 9816–9872.","ieee":"J. A. Keith <i>et al.</i>, “Combining machine learning and computational chemistry for predictive insights into chemical systems,” <i>Chemical Reviews</i>, vol. 121, no. 16. American Chemical Society, pp. 9816–9872, 2021.","apa":"Keith, J. A., Valentin Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger, M., Müller, K.-R., &#38; Tkatchenko, A. (2021). Combining machine learning and computational chemistry for predictive insights into chemical systems. <i>Chemical Reviews</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">https://doi.org/10.1021/acs.chemrev.1c00107</a>","ama":"Keith JA, Valentin Vassilev-Galindo V, Cheng B, et al. Combining machine learning and computational chemistry for predictive insights into chemical systems. <i>Chemical Reviews</i>. 2021;121(16):9816-9872. doi:<a href=\"https://doi.org/10.1021/acs.chemrev.1c00107\">10.1021/acs.chemrev.1c00107</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.chemrev.1c00107"}],"status":"public","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Combining machine learning and computational chemistry for predictive insights into chemical systems","article_type":"review","oa":1,"publication_identifier":{"issn":["0009-2665"],"eissn":["1520-6890"]},"publication":"Chemical Reviews","date_created":"2021-07-20T11:18:37Z","abstract":[{"text":"Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.","lang":"eng"}],"date_updated":"2023-05-08T11:31:03Z","type":"journal_article"},{"tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"e88bb8ca43948abe060eb2d2fa719881","relation":"main_file","file_id":"9944","date_created":"2021-08-19T14:03:48Z","file_name":"Thesis_FeliciangeliA.pdf","date_updated":"2021-09-06T09:28:56Z","creator":"dfelicia","file_size":1958710},{"content_type":"application/octet-stream","checksum":"72810843abee83705853505b3f8348aa","relation":"source_file","access_level":"closed","date_updated":"2022-03-10T12:13:57Z","creator":"dfelicia","file_size":3771669,"date_created":"2021-08-19T14:06:35Z","file_id":"9945","file_name":"thesis.7z"}],"citation":{"short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9733\">https://doi.org/10.15479/at:ista:9733</a>.","mla":"Feliciangeli, Dario. <i>The Polaron at Strong Coupling</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9733\">10.15479/at:ista:9733</a>.","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021.","apa":"Feliciangeli, D. (2021). <i>The polaron at strong coupling</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9733\">https://doi.org/10.15479/at:ista:9733</a>","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9733\">10.15479/at:ista:9733</a>"},"status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"published","ec_funded":1,"doi":"10.15479/at:ista:9733","day":"20","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9787"},{"relation":"part_of_dissertation","id":"9792","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9791"},{"id":"9781","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"9225","status":"public"}]},"corr_author":"1","month":"08","type":"dissertation","date_updated":"2026-04-08T06:59:50Z","file_date_updated":"2022-03-10T12:13:57Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","date_created":"2021-07-27T15:48:30Z","supervisor":[{"orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan"}],"publication_identifier":{"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"oa":1,"has_accepted_license":"1","title":"The polaron at strong coupling","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","year":"2021","degree_awarded":"PhD","ddc":["515","519","539"],"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"publisher":"Institute of Science and Technology Austria","page":"180","article_processing_charge":"No","date_published":"2021-08-20T00:00:00Z","author":[{"orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"_id":"9733"},{"_id":"9746","external_id":{"isi":["000692027800001"],"pmid":["34318749"]},"author":[{"first_name":"Aditi","full_name":"Batra, Aditi","last_name":"Batra"},{"orcid":"0000-0001-9480-5261","first_name":"Roderich","last_name":"Römhild","full_name":"Römhild, Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E"},{"last_name":"Rousseau","full_name":"Rousseau, Emilie","first_name":"Emilie"},{"full_name":"Franzenburg, Sören","last_name":"Franzenburg","first_name":"Sören"},{"first_name":"Stefan","full_name":"Niemann, Stefan","last_name":"Niemann"},{"first_name":"Hinrich","full_name":"Schulenburg, Hinrich","last_name":"Schulenburg"}],"isi":1,"intvolume":"        10","volume":10,"date_published":"2021-07-28T00:00:00Z","pmid":1,"article_processing_charge":"No","publisher":"eLife Sciences Publications","ddc":["570"],"article_number":"e68876","year":"2021","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"High potency of sequential therapy with only beta-lactam antibiotics","oa":1,"abstract":[{"text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.","lang":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication":"eLife","date_created":"2021-07-28T13:36:57Z","date_updated":"2026-06-18T19:56:55Z","type":"journal_article","month":"07","doi":"10.7554/elife.68876","day":"28","department":[{"_id":"CaGu"}],"publication_status":"published","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"status":"public","citation":{"apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., &#38; Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>.","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>, vol. 10, e68876, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>.","short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021)."},"scopus_import":"1","acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel)."},{"oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Ten simple rules to improve academic work- life balance","article_type":"letter_note","type":"journal_article","date_updated":"2025-07-10T12:02:02Z","file_date_updated":"2021-08-05T12:06:49Z","date_created":"2021-08-01T22:01:21Z","publication":"PLoS Computational Biology","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","department":[{"_id":"CaHe"}],"publication_status":"published","day":"15","doi":"10.1371/journal.pcbi.1009124","month":"07","scopus_import":"1","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>.","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>.","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. 2021;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., &#38; Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” <i>PLoS Computational Biology</i>, vol. 17, no. 7. Public Library of Science, 2021."},"file":[{"content_type":"application/pdf","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","relation":"main_file","access_level":"open_access","date_updated":"2021-08-05T12:06:49Z","creator":"cchlebak","file_size":693633,"file_id":"9771","date_created":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf"}],"status":"public","isi":1,"author":[{"first_name":"Michael John","full_name":"Bartlett, Michael John","last_name":"Bartlett"},{"last_name":"Arslan","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","first_name":"Feyza N"},{"first_name":"Adriana","last_name":"Bankston","full_name":"Bankston, Adriana"},{"last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz"}],"_id":"9759","external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"issue":"7","volume":17,"intvolume":"        17","article_processing_charge":"Yes","date_published":"2021-07-15T00:00:00Z","pmid":1,"year":"2021","article_number":"e1009124","ddc":["613"],"publisher":"Public Library of Science"},{"intvolume":"        10","volume":10,"_id":"9761","issue":"7","external_id":{"isi":["000678193300001"],"pmid":["34201955"]},"isi":1,"author":[{"full_name":"Muench, Nicole A.","last_name":"Muench","first_name":"Nicole A."},{"full_name":"Patel, Sonia","last_name":"Patel","first_name":"Sonia"},{"first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","last_name":"Maes"},{"last_name":"Donahue","full_name":"Donahue, Ryan J.","first_name":"Ryan J."},{"full_name":"Ikeda, Akihiro","last_name":"Ikeda","first_name":"Akihiro"},{"last_name":"Nickells","full_name":"Nickells, Robert W.","first_name":"Robert W."}],"ddc":["570"],"publisher":"MDPI","year":"2021","article_number":"1593","date_published":"2021-06-25T00:00:00Z","pmid":1,"article_processing_charge":"Yes","publication":"Cells","date_created":"2021-08-01T22:01:22Z","publication_identifier":{"eissn":["2073-4409"]},"abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}],"type":"journal_article","date_updated":"2026-04-02T13:56:24Z","file_date_updated":"2021-08-04T14:01:30Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","article_type":"original","has_accepted_license":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” <i>Cells</i>, vol. 10, no. 7. MDPI, 2021.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., &#38; Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. 2021;10(7). doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>, vol. 10, no. 7, 1593, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>.","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593."},"file":[{"checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"cziletti","file_size":4555611,"date_updated":"2021-08-04T14:01:30Z","file_name":"2021_Cells_Muench.pdf","file_id":"9768","date_created":"2021-08-04T14:01:30Z"}],"status":"public","scopus_import":"1","acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","publication_status":"published","department":[{"_id":"SaSi"}],"doi":"10.3390/cells10071593","day":"25","month":"06","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1"},{"oa":1,"has_accepted_license":"1","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_updated":"2025-05-14T10:51:56Z","type":"journal_article","file_date_updated":"2021-08-10T11:44:59Z","publication_identifier":{"eissn":["2542-4653"]},"date_created":"2021-08-04T15:00:55Z","publication":"SciPost Physics","abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}],"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"day":"13","doi":"10.21468/scipostphys.11.1.008","ec_funded":1,"publication_status":"published","department":[{"_id":"MiLe"}],"month":"07","scopus_import":"1","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","citation":{"ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>, vol. 11, no. 1, 008, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>.","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., &#38; Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” <i>SciPost Physics</i>, vol. 11, no. 1. SciPost Foundation, 2021."},"file":[{"date_updated":"2021-08-10T11:44:59Z","creator":"asandaue","file_size":1085300,"file_id":"9875","date_created":"2021-08-10T11:44:59Z","file_name":"2021_SciPostPhysics_Brauneis.pdf","content_type":"application/pdf","checksum":"eaa847346b1a023d97bbb291779610ed","relation":"main_file","access_level":"open_access","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"status":"public","author":[{"first_name":"Fabian","full_name":"Brauneis, Fabian","last_name":"Brauneis"},{"last_name":"Hammer","full_name":"Hammer, Hans-Werner","first_name":"Hans-Werner"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"isi":1,"_id":"9769","external_id":{"isi":["000680039500013"],"arxiv":["2101.10958"]},"issue":"1","volume":11,"intvolume":"        11","article_processing_charge":"Yes","date_published":"2021-07-13T00:00:00Z","article_number":"008","year":"2021","ddc":["530"],"publisher":"SciPost Foundation","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}]},{"intvolume":"       104","volume":104,"issue":"2","_id":"9770","external_id":{"isi":["000678780800003"],"arxiv":["2101.05173"]},"author":[{"last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem"},{"first_name":"Hen","full_name":"Alpern, Hen","last_name":"Alpern"},{"first_name":"Yossi","full_name":"Paltiel, Yossi","last_name":"Paltiel"},{"last_name":"Millo","full_name":"Millo, Oded","first_name":"Oded"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg"}],"isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"publisher":"American Physical Society","year":"2021","article_number":"024430","date_published":"2021-07-01T00:00:00Z","article_processing_charge":"No","abstract":[{"text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data.","lang":"eng"}],"publication":"Physical Review B","date_created":"2021-08-04T15:05:32Z","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"type":"journal_article","date_updated":"2025-04-14T07:43:49Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2101.05173","open_access":"1"}],"status":"public","citation":{"apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., &#38; Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. 2021;104(2). doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” <i>Physical Review B</i>, vol. 104, no. 2. American Physical Society, 2021.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430.","short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>.","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>."},"acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","scopus_import":"1","month":"07","department":[{"_id":"MiLe"}],"publication_status":"published","doi":"10.1103/physrevb.104.024430","ec_funded":1,"day":"01","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint"}]