[{"doi":"10.1111/evo.13812","type":"journal_article","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9802"}]},"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"license":"https://creativecommons.org/licenses/by/4.0/","_id":"6680","issue":"9","intvolume":" 73","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:37Z","fulldoi":"https://doi.org/10.1111/evo.13812","corr_author":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","status":"public","date_updated":"2024-10-09T20:58:56Z","volume":73,"oa_version":"Published Version","ddc":["576"],"oa":1,"abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"publisher":"Wiley","citation":{"ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745.","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019."},"day":"01","date_created":"2019-07-25T09:08:28Z","year":"2019","publication":"Evolution","file":[{"date_updated":"2020-07-14T12:47:37Z","file_size":937573,"file_id":"6881","creator":"kschuh","file_name":"2019_Evolution_Sachdeva.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_created":"2019-09-17T10:56:27Z","checksum":"772ce7035965153959b946a1033de1ca"}],"external_id":{"isi":["000481300600001"]},"page":"1729-1745","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","month":"09","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:37Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:6681","corr_author":"1","doi":"10.15479/AT:ISTA:6681","type":"dissertation","publication_status":"published","related_material":{"record":[{"status":"public","id":"6774","relation":"part_of_dissertation"}]},"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"_id":"6681","year":"2019","file":[{"file_name":"Stephan_Zhechev_thesis.pdf","content_type":"application/pdf","relation":"main_file","file_size":1464227,"date_updated":"2020-07-14T12:47:37Z","file_id":"6771","creator":"szhechev","date_created":"2019-08-07T13:02:50Z","access_level":"open_access","checksum":"3231e7cbfca3b5687366f84f0a57a0c0"},{"date_created":"2019-08-07T13:03:22Z","access_level":"closed","checksum":"85d65eb27b4377a9e332ee37a70f08b6","file_name":"Stephan_Zhechev_thesis.tex","content_type":"application/octet-stream","relation":"source_file","file_size":303988,"date_updated":"2020-07-14T12:47:37Z","creator":"szhechev","file_id":"6772"},{"file_name":"supplementary_material.zip","relation":"supplementary_material","content_type":"application/zip","date_updated":"2020-07-14T12:47:37Z","file_size":1087004,"file_id":"6773","creator":"szhechev","access_level":"closed","date_created":"2019-08-07T13:03:34Z","checksum":"86b374d264ca2dd53e712728e253ee75"}],"page":"104","month":"08","date_published":"2019-08-08T00:00:00Z","supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Algorithmic aspects of homotopy theory and embeddability","date_updated":"2026-04-16T12:20:40Z","degree_awarded":"PhD","oa_version":"Published Version","ddc":["514"],"OA_place":"publisher","oa":1,"department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","citation":{"ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019.","apa":"Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681","chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.","short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","mla":"Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria."},"author":[{"full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","first_name":"Stephan Y"}],"date_created":"2019-07-26T11:14:34Z","day":"08"},{"publication_status":"published","doi":"10.1093/aob/mcy183","type":"journal_article","_id":"6710","issue":"7","intvolume":" 123","publication_identifier":{"issn":["0305-7364"],"eissn":["1095-8290"]},"pmid":1,"quality_controlled":"1","article_processing_charge":"No","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1093/aob/mcy183","oa_version":"Published Version","ddc":["570"],"title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","status":"public","date_updated":"2026-06-18T19:11:56Z","volume":123,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"citation":{"ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","apa":"Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183","chicago":"Cossard, Guillaume, Melissa A Toups, and John Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183.","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131.","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183."},"publisher":"Oxford University Press","author":[{"last_name":"Cossard","first_name":"Guillaume","full_name":"Cossard, Guillaume"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups"},{"full_name":"Pannell, John ","first_name":"John ","last_name":"Pannell"}],"day":"04","date_created":"2019-07-28T21:59:15Z","oa":1,"abstract":[{"text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"publication":"Annals of botany","external_id":{"pmid":["30289430"],"isi":["000493043500004"]},"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1119-1131","scopus_import":"1","date_published":"2019-06-04T00:00:00Z","month":"06"},{"isi":1,"fulldoi":"https://doi.org/10.3389/fmicb.2019.01171","file_date_updated":"2020-07-14T12:47:38Z","has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","intvolume":" 10","article_number":"1171","_id":"6717","publication_status":"published","type":"journal_article","doi":"10.3389/fmicb.2019.01171","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"06","date_published":"2019-06-03T00:00:00Z","external_id":{"isi":["000470131200001"]},"project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture"}],"publication":"Frontiers in Microbiology","file":[{"file_id":"6722","creator":"apreinsp","date_updated":"2020-07-14T12:47:38Z","file_size":246151,"relation":"main_file","content_type":"application/pdf","file_name":"2019_Frontiers_Igler.pdf","checksum":"317a06067e9a8e717bb55f23e0d77ba7","access_level":"open_access","date_created":"2019-07-29T07:51:54Z"}],"year":"2019","day":"03","date_created":"2019-07-28T21:59:18Z","publisher":"Frontiers","author":[{"last_name":"Igler","first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abedon, Stephen T.","first_name":"Stephen T.","last_name":"Abedon"}],"citation":{"ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171.","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171","chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.","ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.","apa":"Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171"},"abstract":[{"text":"With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"oa":1,"ddc":["570"],"oa_version":"Published Version","date_updated":"2025-04-14T13:38:17Z","volume":10,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision"},{"fulldoi":"https://doi.org/10.4230/LIPICS.ICALP.2019.77","article_processing_charge":"No","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:38Z","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-109-2"]},"_id":"6725","intvolume":" 132","doi":"10.4230/LIPICS.ICALP.2019.77","type":"conference","publication_status":"published","alternative_title":["LIPIcs"],"page":"77:1-77:12","scopus_import":"1","arxiv":1,"date_published":"2019-07-01T00:00:00Z","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","ec_funded":1,"publication":"46th International Colloquium on Automata, Languages and Programming","file":[{"file_name":"2019_LIPICS_Kolmogorov.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:38Z","file_size":575475,"file_id":"6738","creator":"dernst","access_level":"open_access","date_created":"2019-07-31T07:01:45Z","checksum":"f5ebee8eec6ae09e30365578ee63a492"}],"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"external_id":{"arxiv":["1803.02289"]},"conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2019-07-08","end_date":"2019-07-12","location":"Patras, Greece"},"oa":1,"abstract":[{"text":"A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.","lang":"eng"}],"department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"citation":{"apa":"Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77","ieee":"V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12.","ama":"Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77","chicago":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.","short":"V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.","mla":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77.","ista":"Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov"}],"day":"01","date_created":"2019-07-29T12:23:29Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"Testing the complexity of a valued CSP language","date_updated":"2025-07-10T11:53:47Z","volume":132,"oa_version":"Published Version","ddc":["000"]},{"fulldoi":"https://doi.org/10.1007/978-3-030-23696-0_9","isi":1,"article_processing_charge":"No","editor":[{"first_name":"J","last_name":"Buchmann","full_name":"Buchmann, J"},{"full_name":"Nitaj, A","last_name":"Nitaj","first_name":"A"},{"first_name":"T","last_name":"Rachidi","full_name":"Rachidi, T"}],"quality_controlled":"1","publication_identifier":{"eisbn":["978-3-0302-3696-0"],"isbn":["978-3-0302-3695-3"],"eissn":["1611-3349"],"issn":["0302-9743"]},"_id":"6726","intvolume":" 11627","doi":"10.1007/978-3-030-23696-0_9","type":"book_chapter","publication_status":"published","page":"157-180","scopus_import":"1","date_published":"2019-06-29T00:00:00Z","series_title":"LNCS","month":"06","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2019","ec_funded":1,"publication":"Progress in Cryptology – AFRICACRYPT 2019","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["001299240700009"]},"conference":{"location":"Rabat, Morocco","end_date":"2019-07-11","name":"AFRICACRYPT: International Conference on Cryptology in Africa","start_date":"2019-07-09"},"place":"Cham","oa":1,"abstract":[{"text":"Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so.","lang":"eng"}],"department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/068"}],"citation":{"chicago":"Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi, 11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.","short":"M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.","ama":"Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627. LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9","mla":"Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627, Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9.","ista":"Walter M. 2019.Sampling the integers with low relative error. In: Progress in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.","apa":"Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann, A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019 (Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9","ieee":"M. Walter, “Sampling the integers with low relative error,” in Progress in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T. Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180."},"author":[{"last_name":"Walter","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael"}],"publisher":"Springer Nature","day":"29","date_created":"2019-07-29T12:25:31Z","title":"Sampling the integers with low relative error","status":"public","volume":11627,"date_updated":"2025-09-10T10:38:28Z","oa_version":"Preprint"},{"date_published":"2019-04-01T00:00:00Z","arxiv":1,"month":"04","page":"1051-1060","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","extern":"1","article_processing_charge":"No","conference":{"end_date":"2019-04-18","name":"AISTATS: Artificial Intelligence and Statistics","start_date":"2019-04-16","location":"Naha, Okinawa, Japan"},"external_id":{"arxiv":["1802.07301"]},"quality_controlled":"1","publication":"Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We establish connections between the problem of learning a two-layer neural network and tensor decomposition. We consider a model with feature vectors x∈ℝd, r hidden units with weights {wi}1≤i≤r and output y∈ℝ, i.e., y=∑ri=1σ(w𝖳ix), with activation functions given by low-degree polynomials. In particular, if σ(x)=a0+a1x+a3x3, we prove that no polynomial-time learning algorithm can outperform the trivial predictor that assigns to each example the response variable 𝔼(y), when d3/2≪r≪d2. Our conclusion holds for a `natural data distribution', namely standard Gaussian feature vectors x, and output distributed according to a two-layer neural network with random isotropic weights, and under a certain complexity-theoretic assumption on tensor decomposition. Roughly speaking, we assume that no polynomial-time algorithm can substantially outperform current methods for tensor decomposition based on the sum-of-squares hierarchy. We also prove generalizations of this statement for higher degree polynomial activations, and non-random weight vectors. Remarkably, several existing algorithms for learning two-layer networks with rigorous guarantees are based on tensor decomposition. Our results support the idea that this is indeed the core computational difficulty in learning such networks, under the stated generative model for the data. As a side result, we show that under this model learning the network requires accurate learning of its weights, a property that does not hold in a more general setting. "}],"oa":1,"date_created":"2019-07-31T09:31:26Z","day":"01","intvolume":" 89","publisher":"Proceedings of Machine Learning Research","author":[{"first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"last_name":"Montanari","first_name":"Andrea","full_name":"Montanari, Andrea"}],"citation":{"mla":"Mondelli, Marco, and Andrea Montanari. “On the Connection between Learning Two-Layers Neural Networks and Tensor Decomposition.” Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, vol. 89, Proceedings of Machine Learning Research, 2019, pp. 1051–60.","ista":"Mondelli M, Montanari A. 2019. On the connection between learning two-layers neural networks and tensor decomposition. Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence and Statistics vol. 89, 1051–1060.","ama":"Mondelli M, Montanari A. On the connection between learning two-layers neural networks and tensor decomposition. In: Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics. Vol 89. Proceedings of Machine Learning Research; 2019:1051-1060.","short":"M. Mondelli, A. Montanari, in:, Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, Proceedings of Machine Learning Research, 2019, pp. 1051–1060.","chicago":"Mondelli, Marco, and Andrea Montanari. “On the Connection between Learning Two-Layers Neural Networks and Tensor Decomposition.” In Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 89:1051–60. Proceedings of Machine Learning Research, 2019.","ieee":"M. Mondelli and A. Montanari, “On the connection between learning two-layers neural networks and tensor decomposition,” in Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, Naha, Okinawa, Japan, 2019, vol. 89, pp. 1051–1060.","apa":"Mondelli, M., & Montanari, A. (2019). On the connection between learning two-layers neural networks and tensor decomposition. In Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (Vol. 89, pp. 1051–1060). Naha, Okinawa, Japan: Proceedings of Machine Learning Research."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.07301"}],"_id":"6747","date_updated":"2025-06-26T09:41:13Z","volume":89,"type":"conference","status":"public","title":"On the connection between learning two-layers neural networks and tensor decomposition","oa_version":"Preprint","publication_status":"published"},{"article_type":"original","fulldoi":"https://doi.org/10.1109/TSP.2019.2944738","quality_controlled":"1","article_processing_charge":"No","_id":"6750","issue":"22","article_number":"8854897","intvolume":" 67","publication_identifier":{"issn":["1053-587X"]},"publication_status":"published","doi":"10.1109/TSP.2019.2944738","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_published":"2019-11-15T00:00:00Z","month":"11","arxiv":1,"publication":"IEEE Transactions on Signal Processing","external_id":{"arxiv":["1903.09203"]},"year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1903.09203","open_access":"1"}],"citation":{"ista":"Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 67(22), 8854897.","mla":"Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738.","short":"S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal Processing 67 (2019).","chicago":"Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019. https://doi.org/10.1109/TSP.2019.2944738.","ama":"Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738","ieee":"S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22. IEEE, 2019.","apa":"Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738"},"publisher":"IEEE","author":[{"full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali","last_name":"Hashemi"},{"full_name":"Condo, Carlo","last_name":"Condo","first_name":"Carlo"},{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli"},{"last_name":"Gross","first_name":"Warren J","full_name":"Gross, Warren J"}],"day":"15","date_created":"2019-07-31T09:51:14Z","oa":1,"abstract":[{"lang":"eng","text":"Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. "}],"department":[{"_id":"MaMo"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","title":"Rate-flexible fast polar decoders","status":"public","date_updated":"2025-01-14T14:34:26Z","volume":67},{"isi":1,"fulldoi":"https://doi.org/10.1145/3340295","quality_controlled":"1","article_processing_charge":"No","intvolume":" 66","article_number":"31","_id":"6752","issue":"4","publication_identifier":{"issn":["0004-5411"],"eissn":["1557-735X"]},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"950"}]},"publication_status":"published","type":"journal_article","doi":"10.1145/3340295","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_published":"2019-07-16T00:00:00Z","month":"07","arxiv":1,"project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"}],"external_id":{"isi":["000487714900008"],"arxiv":["1705.01433"]},"publication":"Journal of the ACM","year":"2019","day":"16","date_created":"2019-08-04T21:59:16Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.01433"}],"author":[{"first_name":"Guy","last_name":"Avni","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"}],"publisher":"ACM","citation":{"ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. Journal of the ACM. 2019;66(4). doi:10.1145/3340295","chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3340295.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, Journal of the ACM 66 (2019).","mla":"Avni, Guy, et al. “Infinite-Duration Bidding Games.” Journal of the ACM, vol. 66, no. 4, 31, ACM, 2019, doi:10.1145/3340295.","ista":"Avni G, Henzinger TA, Chonev VK. 2019. Infinite-duration bidding games. Journal of the ACM. 66(4), 31.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2019). Infinite-duration bidding games. Journal of the ACM. ACM. https://doi.org/10.1145/3340295","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” Journal of the ACM, vol. 66, no. 4. ACM, 2019."},"abstract":[{"lang":"eng","text":"Two-player games on graphs are widely studied in formal methods, as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. The following bidding rule was previously defined and called Richman bidding. Both players have separate budgets, which sum up to 1. In each turn, a bidding takes place: Both players submit bids simultaneously, where a bid is legal if it does not exceed the available budget, and the higher bidder pays his bid to the other player and moves the token. The central question studied in bidding games is a necessary and sufficient initial budget for winning the game: a threshold budget in a vertex is a value t ∈ [0, 1] such that if Player 1’s budget exceeds t, he can win the game; and if Player 2’s budget exceeds 1 − t, he can win the game. Threshold budgets were previously shown to exist in every vertex of a reachability game, which have an interesting connection with random-turn games—a sub-class of simple stochastic games in which the player who moves is chosen randomly. We show the existence of threshold budgets for a qualitative class of infinite-duration games, namely parity games, and a quantitative class, namely mean-payoff games. The key component of the proof is a quantitative solution to strongly connected mean-payoff bidding games in which we extend the connection with random-turn games to these games, and construct explicit optimal strategies for both players."}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"oa":1,"oa_version":"Preprint","volume":66,"date_updated":"2025-07-10T11:53:47Z","title":"Infinite-duration bidding games","status":"public"},{"external_id":{"isi":["000484039500018"],"pmid":["31273378"]},"file":[{"access_level":"open_access","date_created":"2019-08-05T07:55:02Z","checksum":"f9e8f6863a406dcc5a36b2be001c138c","file_name":"2019_GenomeBiology_Picard.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:39Z","file_size":580205,"creator":"dernst","file_id":"6765"}],"publication":"Genome biology and evolution","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","month":"07","page":"1909-1922","ddc":["570"],"acknowledged_ssus":[{"_id":"CampIT"}],"oa_version":"Published Version","date_updated":"2025-05-14T11:08:50Z","volume":11,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","day":"01","date_created":"2019-08-04T21:59:18Z","publisher":"Oxford University Press","author":[{"full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A L"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"last_name":"Roquis","first_name":"David","full_name":"Roquis, David"},{"last_name":"Bulla","first_name":"Ingo","full_name":"Bulla, Ingo"},{"last_name":"Augusto","first_name":"Ronaldo C.","full_name":"Augusto, Ronaldo C."},{"first_name":"Nathalie","last_name":"Arancibia","full_name":"Arancibia, Nathalie"},{"first_name":"Christoph","last_name":"Grunau","full_name":"Grunau, Christoph"},{"first_name":"Jérôme","last_name":"Boissier","full_name":"Boissier, Jérôme"},{"full_name":"Cosseau, Céline","last_name":"Cosseau","first_name":"Céline"}],"citation":{"ieee":"M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford University Press, pp. 1909–1922, 2019.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz133","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz133.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford University Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922."},"abstract":[{"text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"oa":1,"file_date_updated":"2020-07-14T12:47:39Z","has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1093/gbe/evz133","publication_status":"published","type":"journal_article","doi":"10.1093/gbe/evz133","intvolume":" 11","_id":"6755","issue":"7","pmid":1,"publication_identifier":{"eissn":["1759-6653"]}},{"abstract":[{"text":"We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. \r\nWe also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.","lang":"eng"}],"department":[{"_id":"DaAl"}],"language":[{"iso":"eng"}],"oa":1,"day":"19","date_created":"2019-08-04T21:59:20Z","citation":{"short":"V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).","chicago":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2019. https://doi.org/10.37236/8096.","ama":"Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 2019;26(3). doi:10.37236/8096","mla":"Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.” Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic Journal of Combinatorics, 2019, doi:10.37236/8096.","ista":"Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. 26(3), P3.17.","ieee":"V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics, 2019.","apa":"Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/8096"},"publisher":"Electronic Journal of Combinatorics","author":[{"full_name":"Jelínek, Vít","last_name":"Jelínek","first_name":"Vít"},{"last_name":"Töpfer","first_name":"Martin","id":"4B865388-F248-11E8-B48F-1D18A9856A87","full_name":"Töpfer, Martin"}],"volume":26,"date_updated":"2025-06-26T12:25:39Z","title":"On grounded L-graphs and their relatives","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","ddc":["510"],"OA_place":"publisher","oa_version":"Published Version","scopus_import":"1","month":"07","arxiv":1,"date_published":"2019-07-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"year":"2019","external_id":{"arxiv":["1808.04148"]},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file":[{"date_updated":"2020-07-14T12:47:39Z","file_size":533697,"creator":"dernst","file_id":"6764","file_name":"2019_eJourCombinatorics_Jelinek.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2019-08-05T06:46:55Z","access_level":"open_access","checksum":"20fc366fc6683ef0b074a019b73a663a"}],"publication":"Electronic Journal of Combinatorics","publication_identifier":{"eissn":["1077-8926"]},"article_number":"P3.17","intvolume":" 26","OA_type":"gold","_id":"6759","issue":"3","type":"journal_article","doi":"10.37236/8096","publication_status":"published","article_type":"original","fulldoi":"https://doi.org/10.37236/8096","DOAJ_listed":"1","corr_author":"1","article_processing_charge":"Yes","file_date_updated":"2020-07-14T12:47:39Z","has_accepted_license":"1","quality_controlled":"1"},{"fulldoi":"https://doi.org/10.1137/18M1207272","isi":1,"article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["1540-3459"],"eissn":["1540-3467"]},"issue":"3","_id":"6762","intvolume":" 17","doi":"10.1137/18M1207272","type":"journal_article","publication_status":"published","page":"926-947","date_published":"2019-07-16T00:00:00Z","month":"07","arxiv":1,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publication":"Multiscale Modeling and Simulation","external_id":{"isi":["000487931800002"],"arxiv":["1808.04200"]},"oa":1,"department":[{"_id":"JuFi"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size."}],"publisher":"SIAM","citation":{"ista":"Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947.","mla":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272.","ama":"Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272","chicago":"Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272.","short":"G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947.","apa":"Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272","ieee":"G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019."},"author":[{"last_name":"Friesecke","first_name":"Gero","full_name":"Friesecke, Gero"},{"orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael","first_name":"Michael","last_name":"Kniely"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04200"}],"date_created":"2019-08-04T21:59:21Z","day":"16","status":"public","title":"New optimal control problems in density functional theory motivated by photovoltaics","volume":17,"date_updated":"2025-07-10T11:53:49Z","oa_version":"Preprint"},{"date_created":"2019-08-04T21:59:21Z","day":"15","author":[{"full_name":"Khattak, Hamza K.","first_name":"Hamza K.","last_name":"Khattak"},{"first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"},{"full_name":"Slepkov, Aaron D.","last_name":"Slepkov","first_name":"Aaron D."}],"citation":{"mla":"Khattak, Hamza K., et al. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter, vol. 15, no. 29, Royal Society of Chemistry, 2019, pp. 5804–09, doi:10.1039/c9sm00756c.","ista":"Khattak HK, Waitukaitis SR, Slepkov AD. 2019. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 15(29), 5804–5809.","ama":"Khattak HK, Waitukaitis SR, Slepkov AD. Microwave induced mechanical activation of hydrogel dimers. Soft Matter. 2019;15(29):5804-5809. doi:10.1039/c9sm00756c","short":"H.K. Khattak, S.R. Waitukaitis, A.D. Slepkov, Soft Matter 15 (2019) 5804–5809.","chicago":"Khattak, Hamza K., Scott R Waitukaitis, and Aaron D. Slepkov. “Microwave Induced Mechanical Activation of Hydrogel Dimers.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c9sm00756c.","ieee":"H. K. Khattak, S. R. Waitukaitis, and A. D. Slepkov, “Microwave induced mechanical activation of hydrogel dimers,” Soft Matter, vol. 15, no. 29. Royal Society of Chemistry, pp. 5804–5809, 2019.","apa":"Khattak, H. K., Waitukaitis, S. R., & Slepkov, A. D. (2019). Microwave induced mechanical activation of hydrogel dimers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c9sm00756c"},"publisher":"Royal Society of Chemistry","department":[{"_id":"ScWa"}],"language":[{"iso":"eng"}],"abstract":[{"text":"When grape-sized aqueous dimers are irradiated in a microwave oven, an intense electromagnetic hotspot forms at their point of contact, often igniting a plasma. Here we show that this irradiation can result in the injection of mechanical energy. By examining irradiated hydrogel dimers through high-speed imaging, we find that they repeatedly bounce off of each other while irradiated. We determine that an average of 1 lJ of mechanical energy is injected into the pair during each collision. Furthermore, a characteristic high-pitched audio signal is found to accompany each collision.\r\nWe show that both the audio signal and the energy injection arise via an interplay between vaporization and elastic deformations in the region of contact, the so-called ‘elastic Liedenfrost effect’. Our results establish a novel, non-contact method of injecting mechanical energy into soft matter systems, suggesting application in fields such as soft robotics.","lang":"eng"}],"oa_version":"None","date_updated":"2025-07-10T11:53:49Z","volume":15,"status":"public","title":"Microwave induced mechanical activation of hydrogel dimers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_published":"2019-07-15T00:00:00Z","scopus_import":"1","page":"5804-5809","external_id":{"isi":["000476909200002"],"pmid":["31305853"]},"publication":"Soft Matter","year":"2019","intvolume":" 15","issue":"29","_id":"6763","pmid":1,"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"publication_status":"published","type":"journal_article","doi":"10.1039/c9sm00756c","isi":1,"fulldoi":"https://doi.org/10.1039/c9sm00756c","article_type":"original","quality_controlled":"1","article_processing_charge":"No"},{"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/when-plant-roots-learned-to-follow-gravity/","description":"News on IST Homepage"}]},"publication_status":"published","type":"journal_article","doi":"10.1038/s41467-019-11471-8","article_number":"3480","intvolume":" 10","_id":"6778","pmid":1,"publication_identifier":{"issn":["2041-1723"]},"file_date_updated":"2020-07-14T12:47:40Z","has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1038/s41467-019-11471-8","ddc":["580"],"oa_version":"Published Version","volume":10,"date_updated":"2025-04-14T07:45:04Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Evolution of fast root gravitropism in seed plants","day":"02","date_created":"2019-08-09T08:46:26Z","publisher":"Springer Nature","citation":{"ista":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. 2019. Evolution of fast root gravitropism in seed plants. Nature Communications. 10, 3480.","mla":"Zhang, Yuzhou, et al. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications, vol. 10, 3480, Springer Nature, 2019, doi:10.1038/s41467-019-11471-8.","chicago":"Zhang, Yuzhou, G Xiao, X Wang, Xixi Zhang, and Jiří Friml. “Evolution of Fast Root Gravitropism in Seed Plants.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11471-8.","short":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, J. Friml, Nature Communications 10 (2019).","ama":"Zhang Y, Xiao G, Wang X, Zhang X, Friml J. Evolution of fast root gravitropism in seed plants. Nature Communications. 2019;10. doi:10.1038/s41467-019-11471-8","apa":"Zhang, Y., Xiao, G., Wang, X., Zhang, X., & Friml, J. (2019). Evolution of fast root gravitropism in seed plants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11471-8","ieee":"Y. Zhang, G. Xiao, X. Wang, X. Zhang, and J. Friml, “Evolution of fast root gravitropism in seed plants,” Nature Communications, vol. 10. Springer Nature, 2019."},"author":[{"orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang"},{"full_name":"Xiao, G","first_name":"G","last_name":"Xiao"},{"last_name":"Wang","first_name":"X","full_name":"Wang, X"},{"first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"abstract":[{"lang":"eng","text":"An important adaptation during colonization of land by plants is gravitropic growth of roots, which enabled roots to reach water and nutrients, and firmly anchor plants in the ground. Here we provide insights into the evolution of an efficient root gravitropic mechanism in the seed plants. Architectural innovation, with gravity perception constrained in the root tips\r\nalong with a shootward transport route for the phytohormone auxin, appeared only upon the emergence of seed plants. Interspecies complementation and protein domain swapping revealed functional innovations within the PIN family of auxin transporters leading to the evolution of gravitropism-specific PINs. The unique apical/shootward subcellular localization of PIN proteins is the major evolutionary innovation that connected the anatomically separated sites of gravity perception and growth response via the mobile auxin signal. We conclude that the crucial anatomical and functional components emerged hand-in-hand to facilitate the evolution of fast gravitropic response, which is one of the major adaptations of seed plants to dry land."}],"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"oa":1,"external_id":{"pmid":["31375675"],"isi":["000478576500012"]},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"publication":"Nature Communications","file":[{"checksum":"d2c654fdb97f33078f606fe0c298bf6e","access_level":"open_access","date_created":"2019-08-12T07:09:20Z","relation":"main_file","content_type":"application/pdf","file_name":"2019_NatureComm_Zhang.pdf","creator":"dernst","file_id":"6798","file_size":6406141,"date_updated":"2020-07-14T12:47:40Z"}],"ec_funded":1,"year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","date_published":"2019-08-02T00:00:00Z","month":"08"},{"ddc":["532"],"oa_version":"Preprint","date_updated":"2025-04-15T06:50:28Z","volume":100,"status":"public","title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","day":"25","date_created":"2019-08-09T09:40:41Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.05860"}],"author":[{"first_name":"Balachandra","last_name":"Suri","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pallantla, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Pallantla"},{"full_name":"Schatz, Michael F.","first_name":"Michael F.","last_name":"Schatz"},{"last_name":"Grigoriev","first_name":"Roman O.","full_name":"Grigoriev, Roman O."}],"citation":{"ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112.","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019.","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112"},"publisher":"American Physical Society","abstract":[{"text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"publication":"Physical Review E","ec_funded":1,"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_published":"2019-07-25T00:00:00Z","arxiv":1,"month":"07","publication_status":"published","type":"journal_article","doi":"10.1103/physreve.100.013112","intvolume":" 100","article_number":"013112","_id":"6779","issue":"1","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"quality_controlled":"1","article_processing_charge":"No","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1103/physreve.100.013112"},{"scopus_import":"1","date_published":"2019-07-02T00:00:00Z","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","external_id":{"isi":["000481577700032"]},"project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems"}],"publication":"PLoS Computational Biology","file":[{"access_level":"open_access","date_created":"2019-08-12T12:27:26Z","checksum":"7ded4721b41c2a0fc66a1c634540416a","date_updated":"2020-07-14T12:47:40Z","file_size":2200003,"file_id":"6803","creator":"dernst","file_name":"2019_PlosComputBiology_Ruess.pdf","relation":"main_file","content_type":"application/pdf"}],"abstract":[{"text":"Mathematical models have been used successfully at diverse scales of biological organization, ranging from ecology and population dynamics to stochastic reaction events occurring between individual molecules in single cells. Generally, many biological processes unfold across multiple scales, with mutations being the best studied example of how stochasticity at the molecular scale can influence outcomes at the population scale. In many other contexts, however, an analogous link between micro- and macro-scale remains elusive, primarily due to the challenges involved in setting up and analyzing multi-scale models. Here, we employ such a model to investigate how stochasticity propagates from individual biochemical reaction events in the bacterial innate immune system to the ecology of bacteria and bacterial viruses. We show analytically how the dynamics of bacterial populations are shaped by the activities of immunity-conferring enzymes in single cells and how the ecological consequences imply optimal bacterial defense strategies against viruses. Our results suggest that bacterial populations in the presence of viruses can either optimize their initial growth rate or their population size, with the first strategy favoring simple immunity featuring a single restriction modification system and the second strategy favoring complex bacterial innate immunity featuring several simultaneously active restriction modification systems.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"oa":1,"day":"02","date_created":"2019-08-11T21:59:19Z","publisher":"Public Library of Science","author":[{"last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob"},{"last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper"}],"citation":{"ieee":"J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Molecular noise of innate immunity shapes bacteria-phage ecologies,” PLoS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","apa":"Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168","ama":"Ruess J, Pleska M, Guet CC, Tkačik G. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007168","chicago":"Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.","short":"J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, PLoS Computational Biology 15 (2019).","ista":"Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Molecular noise of innate immunity shapes bacteria-phage ecologies. PLoS Computational Biology. 15(7), e1007168.","mla":"Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168."},"date_updated":"2025-04-14T13:46:26Z","volume":15,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"Molecular noise of innate immunity shapes bacteria-phage ecologies","ddc":["570"],"oa_version":"Published Version","article_type":"original","fulldoi":"https://doi.org/10.1371/journal.pcbi.1007168","isi":1,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:40Z","has_accepted_license":"1","quality_controlled":"1","publication_identifier":{"eissn":["1553-7358"]},"article_number":"e1007168","intvolume":" 15","_id":"6784","issue":"7","type":"journal_article","doi":"10.1371/journal.pcbi.1007168","related_material":{"record":[{"relation":"research_data","status":"public","id":"9786"}]},"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","arxiv":1,"date_published":"2019-05-08T00:00:00Z","month":"05","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1807.11238"],"isi":["000467402900001"]},"publication":"Physical Review X","file":[{"checksum":"065ff82ee4a1d2c3773ce4b76ff4213c","date_created":"2019-08-12T12:14:18Z","access_level":"open_access","creator":"dernst","file_id":"6802","date_updated":"2020-07-14T12:47:40Z","file_size":1193550,"content_type":"application/pdf","relation":"main_file","file_name":"2019_PhysReviewX_Hubert.pdf"}],"year":"2019","day":"08","date_created":"2019-08-11T21:59:20Z","publisher":"American Physical Society","author":[{"full_name":"Hubert, Colin","first_name":"Colin","last_name":"Hubert"},{"full_name":"Baruchi, Yifat","last_name":"Baruchi","first_name":"Yifat"},{"full_name":"Mazuz-Harpaz, Yotam","first_name":"Yotam","last_name":"Mazuz-Harpaz"},{"full_name":"Cohen, Kobi","last_name":"Cohen","first_name":"Kobi"},{"full_name":"Biermann, Klaus","first_name":"Klaus","last_name":"Biermann"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"full_name":"West, Ken","first_name":"Ken","last_name":"West"},{"full_name":"Pfeiffer, Loren","last_name":"Pfeiffer","first_name":"Loren"},{"full_name":"Rapaport, Ronen","first_name":"Ronen","last_name":"Rapaport"},{"last_name":"Santos","first_name":"Paulo","full_name":"Santos, Paulo"}],"citation":{"ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026.","short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026.","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026","ieee":"C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019."},"abstract":[{"lang":"eng","text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations."}],"department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"oa":1,"ddc":["530"],"oa_version":"Published Version","volume":9,"date_updated":"2025-04-15T07:59:29Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Attractive dipolar coupling between stacked exciton fluids","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1103/PhysRevX.9.021026","file_date_updated":"2020-07-14T12:47:40Z","has_accepted_license":"1","quality_controlled":"1","article_processing_charge":"No","intvolume":" 9","article_number":"021026","_id":"6786","issue":"2","publication_identifier":{"eissn":["2160-3308"]},"publication_status":"published","type":"journal_article","doi":"10.1103/PhysRevX.9.021026"},{"issue":"5","_id":"6793","intvolume":" 51","publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]},"publication_status":"published","doi":"10.1112/blms.12276","type":"journal_article","isi":1,"fulldoi":"https://doi.org/10.1112/blms.12276","article_type":"original","quality_controlled":"1","article_processing_charge":"No","publisher":"London Mathematical Society","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Izmestiev, Ivan","last_name":"Izmestiev","first_name":"Ivan"}],"citation":{"ama":"Akopyan A, Izmestiev I. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 2019;51(5):765-775. doi:10.1112/blms.12276","chicago":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society. London Mathematical Society, 2019. https://doi.org/10.1112/blms.12276.","short":"A. Akopyan, I. Izmestiev, Bulletin of the London Mathematical Society 51 (2019) 765–775.","mla":"Akopyan, Arseniy, and Ivan Izmestiev. “The Regge Symmetry, Confocal Conics, and the Schläfli Formula.” Bulletin of the London Mathematical Society, vol. 51, no. 5, London Mathematical Society, 2019, pp. 765–75, doi:10.1112/blms.12276.","ista":"Akopyan A, Izmestiev I. 2019. The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. 51(5), 765–775.","ieee":"A. Akopyan and I. Izmestiev, “The Regge symmetry, confocal conics, and the Schläfli formula,” Bulletin of the London Mathematical Society, vol. 51, no. 5. London Mathematical Society, pp. 765–775, 2019.","apa":"Akopyan, A., & Izmestiev, I. (2019). The Regge symmetry, confocal conics, and the Schläfli formula. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12276"},"main_file_link":[{"url":"https://arxiv.org/abs/1903.04929","open_access":"1"}],"date_created":"2019-08-11T21:59:23Z","day":"01","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"abstract":[{"text":"The Regge symmetry is a set of remarkable relations between two tetrahedra whose edge lengths are related in a simple fashion. It was first discovered as a consequence of an asymptotic formula in mathematical physics. Here, we give a simple geometric proof of Regge symmetries in Euclidean, spherical, and hyperbolic geometry.","lang":"eng"}],"oa_version":"Preprint","title":"The Regge symmetry, confocal conics, and the Schläfli formula","status":"public","date_updated":"2025-07-10T11:53:52Z","volume":51,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"765-775","date_published":"2019-10-01T00:00:00Z","arxiv":1,"month":"10","scopus_import":"1","publication":"Bulletin of the London Mathematical Society","external_id":{"isi":["000478560200001"],"arxiv":["1903.04929"]},"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"year":"2019","ec_funded":1},{"publication_identifier":{"eissn":["2045-7758"]},"intvolume":" 9","_id":"6795","issue":"17","type":"journal_article","doi":"10.1002/ece3.5484","publication_status":"published","article_type":"original","fulldoi":"https://doi.org/10.1002/ece3.5484","isi":1,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:40Z","has_accepted_license":"1","quality_controlled":"1","abstract":[{"text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"oa":1,"day":"01","date_created":"2019-08-11T21:59:24Z","author":[{"first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"citation":{"ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484","mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484."},"publisher":"Wiley","volume":9,"date_updated":"2026-04-03T09:50:31Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Green beards in the light of indirect genetic effects","status":"public","ddc":["576"],"oa_version":"Published Version","scopus_import":"1","month":"09","date_published":"2019-09-01T00:00:00Z","page":"9597-9608","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"year":"2019","project":[{"name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"}],"external_id":{"isi":["000479973400001"]},"publication":"Ecology and Evolution","file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2019_EcologyEvolution_Trubenova.pdf","file_id":"6799","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":2839636,"checksum":"adcb70af4901977d95b8747eeee01bd7","date_created":"2019-08-12T07:30:30Z","access_level":"open_access"}]},{"fulldoi":"https://doi.org/10.1016/j.dyepig.2019.107768","article_type":"original","isi":1,"article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0143-7208"]},"intvolume":" 171","article_number":"107768","_id":"6818","type":"journal_article","doi":"10.1016/j.dyepig.2019.107768","publication_status":"published","date_published":"2019-12-01T00:00:00Z","month":"12","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","external_id":{"isi":["000484870700099"]},"publication":"Dyes and Pigments","department":[{"_id":"MaIb"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Indigoidine is a blue natural pigment, which can be efficiently synthetized in E. coli. In addition to its antioxidant and antimicrobial activities indigoidine due to its stability and deep blue color can find an application as an industrial, environmentally friendly dye. Moreover, similarly to its counterpart regular indigo dye, due to its molecular structure, indigoidine is an organic semiconductor. Fully conjugated aromatic moiety and intermolecular hydrogen bonding of indigoidine result in an unusually narrow bandgap for such a small molecule. This, in its turn, result is tight molecular packing in the solid state and opens a path for a wide range of application in organic and bio-electronics, such as electrochemical and field effect transistors, organic solar cells, light and bio-sensors etc."}],"date_created":"2019-08-18T22:00:39Z","day":"01","citation":{"ama":"Yumusak C, Prochazkova AJ, Apaydin DH, et al. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 2019;171. doi:10.1016/j.dyepig.2019.107768","short":"C. Yumusak, A.J. Prochazkova, D.H. Apaydin, H. Seelajaroen, N.S. Sariciftci, M. Weiter, J. Krajcovic, Y. Qin, W. Zhang, J. Zhan, A. Kovalenko, Dyes and Pigments 171 (2019).","chicago":"Yumusak, Cigdem, Anna Jancik Prochazkova, Dogukan H Apaydin, Hathaichanok Seelajaroen, Niyazi Serdar Sariciftci, Martin Weiter, Jozef Krajcovic, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” Dyes and Pigments. Elsevier, 2019. https://doi.org/10.1016/j.dyepig.2019.107768.","ista":"Yumusak C, Prochazkova AJ, Apaydin DH, Seelajaroen H, Sariciftci NS, Weiter M, Krajcovic J, Qin Y, Zhang W, Zhan J, Kovalenko A. 2019. Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. 171, 107768.","mla":"Yumusak, Cigdem, et al. “Indigoidine - Biosynthesized Organic Semiconductor.” Dyes and Pigments, vol. 171, 107768, Elsevier, 2019, doi:10.1016/j.dyepig.2019.107768.","ieee":"C. Yumusak et al., “Indigoidine - Biosynthesized organic semiconductor,” Dyes and Pigments, vol. 171. Elsevier, 2019.","apa":"Yumusak, C., Prochazkova, A. J., Apaydin, D. H., Seelajaroen, H., Sariciftci, N. S., Weiter, M., … Kovalenko, A. (2019). Indigoidine - Biosynthesized organic semiconductor. Dyes and Pigments. Elsevier. https://doi.org/10.1016/j.dyepig.2019.107768"},"author":[{"full_name":"Yumusak, Cigdem","first_name":"Cigdem","last_name":"Yumusak"},{"first_name":"Anna Jancik","last_name":"Prochazkova","full_name":"Prochazkova, Anna Jancik"},{"orcid":"0000-0002-1075-8857","id":"2FF891BC-F248-11E8-B48F-1D18A9856A87","full_name":"Apaydin, Dogukan H","last_name":"Apaydin","first_name":"Dogukan H"},{"first_name":"Hathaichanok","last_name":"Seelajaroen","full_name":"Seelajaroen, Hathaichanok"},{"last_name":"Sariciftci","first_name":"Niyazi Serdar","full_name":"Sariciftci, Niyazi Serdar"},{"first_name":"Martin","last_name":"Weiter","full_name":"Weiter, Martin"},{"full_name":"Krajcovic, Jozef","last_name":"Krajcovic","first_name":"Jozef"},{"full_name":"Qin, Yong","first_name":"Yong","last_name":"Qin"},{"first_name":"Wei","last_name":"Zhang","full_name":"Zhang, Wei"},{"full_name":"Zhan, Jixun","first_name":"Jixun","last_name":"Zhan"},{"full_name":"Kovalenko, Alexander","last_name":"Kovalenko","first_name":"Alexander"}],"publisher":"Elsevier","date_updated":"2023-08-29T07:11:09Z","volume":171,"status":"public","title":"Indigoidine - Biosynthesized organic semiconductor","oa_version":"None"}]