[{"author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"last_name":"Cieplak","first_name":"Marek","full_name":"Cieplak, Marek"},{"full_name":"Carrión Vázquez, Mariano","first_name":"Mariano","last_name":"Carrión Vázquez"}],"article_processing_charge":"No","month":"10","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1566"}]},"department":[{"_id":"CaHe"}],"year":"2015","date_created":"2021-07-23T12:05:28Z","doi":"10.1371/journal.pcbi.1004541.s001","citation":{"mla":"Gómez Sicilia, Àngel, et al. <i>An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., &#38; Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures - submission to PLOS journals. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">https://doi.org/10.1371/journal.pcbi.1004541.s001</a>","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).","ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures - submission to PLOS journals. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures - submission to PLOS journals.” Public Library of Science, 2015.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures - submission to PLOS journals, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">10.1371/journal.pcbi.1004541.s001</a>.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission to PLOS Journals.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541.s001\">https://doi.org/10.1371/journal.pcbi.1004541.s001</a>."},"status":"public","oa_version":"Published Version","day":"23","_id":"9714","title":"An exploration of the universe of polyglutamine structures - submission to PLOS journals","type":"research_data_reference","fulldoi":"https://doi.org/10.1371/journal.pcbi.1004541.s001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-10-23T00:00:00Z","date_updated":"2026-07-06T13:54:29Z","publisher":"Public Library of Science"},{"volume":14,"page":"980 - 1017","oa_version":"Published Version","publication_status":"published","main_file_link":[{"url":"http://discovery.ucl.ac.uk/1473750/1/99393.pdf","open_access":"1"}],"scopus_import":"1","publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","ec_funded":1,"fulldoi":"https://doi.org/10.1137/140993934","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations.","lang":"eng"}],"article_type":"original","publication":"SIAM Journal on Applied Dynamical Systems","project":[{"call_identifier":"FP7","_id":"255F06BE-B435-11E9-9278-68D0E5697425","grant_number":"622033","name":"Persistent Homology - Images, Data and Maps"}],"acknowledgement":"Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project.","doi":"10.1137/140993934","publist_id":"5616","title":"Rich bifurcation structure in a two patch vaccination model","issue":"2","isi":1,"day":"01","_id":"1555","language":[{"iso":"eng"}],"intvolume":"        14","publication_identifier":{"eissn":["1536-0040"]},"das_tickbox":"1","ddc":["510"],"date_published":"2015-01-01T00:00:00Z","date_updated":"2026-07-06T13:59:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","external_id":{"isi":["000357310400015"]},"author":[{"first_name":"Diána","last_name":"Knipl","full_name":"Knipl, Diána"},{"full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","last_name":"Pilarczyk","first_name":"Pawel"},{"first_name":"Gergely","last_name":"Röst","full_name":"Röst, Gergely"}],"oa":1,"status":"public","department":[{"_id":"HeEd"}],"year":"2015","citation":{"mla":"Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2, Society for Industrial and Applied Mathematics, 2015, pp. 980–1017, doi:<a href=\"https://doi.org/10.1137/140993934\">10.1137/140993934</a>.","ama":"Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. <i>SIAM Journal on Applied Dynamical Systems</i>. 2015;14(2):980-1017. doi:<a href=\"https://doi.org/10.1137/140993934\">10.1137/140993934</a>","short":"D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017.","apa":"Knipl, D., Pilarczyk, P., &#38; Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>","chicago":"Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” <i>SIAM Journal on Applied Dynamical Systems</i>. Society for Industrial and Applied Mathematics, 2015. <a href=\"https://doi.org/10.1137/140993934\">https://doi.org/10.1137/140993934</a>.","ista":"Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017.","ieee":"D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” <i>SIAM Journal on Applied Dynamical Systems</i>, vol. 14, no. 2. Society for Industrial and Applied Mathematics, pp. 980–1017, 2015."},"date_created":"2018-12-11T11:52:42Z"},{"publication_status":"published","oa_version":"Preprint","page":"52 - 59","volume":115,"ec_funded":1,"fulldoi":"https://doi.org/10.1016/j.ipl.2014.09.001","type":"journal_article","publisher":"Elsevier","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.4225"}],"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"Information Processing Letters","abstract":[{"lang":"eng","text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers."}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1016/j.ipl.2014.09.001","_id":"2034","language":[{"iso":"eng"}],"day":"01","issue":"1","isi":1,"title":"Probabilistic opacity for Markov decision processes","publist_id":"5025","arxiv":1,"date_published":"2015-01-01T00:00:00Z","date_updated":"2026-07-07T13:10:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","das_tickbox":"1","intvolume":"       115","oa":1,"author":[{"first_name":"Béatrice","last_name":"Bérard","full_name":"Bérard, Béatrice"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Sznajder, Nathalie","last_name":"Sznajder","first_name":"Nathalie"}],"external_id":{"arxiv":["1407.4225"],"isi":["000345478700010"]},"month":"01","date_created":"2018-12-11T11:55:20Z","citation":{"short":"B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115 (2015) 52–59.","apa":"Bérard, B., Chatterjee, K., &#38; Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>","ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. <i>Information Processing Letters</i>. 2015;115(1):52-59. doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” <i>Information Processing Letters</i>, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>.","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” <i>Information Processing Letters</i>, vol. 115, no. 1. Elsevier, pp. 52–59, 2015.","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” <i>Information Processing Letters</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>."},"year":"2015","department":[{"_id":"KrCh"}],"status":"public"},{"status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2015","citation":{"apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i>Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i>Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>."},"date_created":"2018-12-11T11:52:37Z","month":"10","external_id":{"isi":["000362056300005"]},"author":[{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"first_name":"Golnaz","last_name":"Badkobeh","full_name":"Badkobeh, Golnaz"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Çörüş, Doğan","first_name":"Doğan","last_name":"Çörüş"},{"full_name":"Dang, Duccuong","first_name":"Duccuong","last_name":"Dang"},{"full_name":"Friedrich, Tobias","first_name":"Tobias","last_name":"Friedrich"},{"full_name":"Lehre, Per","first_name":"Per","last_name":"Lehre"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"first_name":"Andrew","last_name":"Sutton","full_name":"Sutton, Andrew"},{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"}],"has_accepted_license":"1","oa":1,"intvolume":"       383","file_date_updated":"2020-07-14T12:45:01Z","das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-07T13:12:13Z","ddc":["570"],"date_published":"2015-10-21T00:00:00Z","publist_id":"5629","title":"Toward a unifying framework for evolutionary processes","isi":1,"day":"21","language":[{"iso":"eng"}],"_id":"1542","file":[{"date_created":"2018-12-12T10:16:53Z","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","content_type":"application/pdf","file_id":"5244","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","creator":"system","file_size":595307,"relation":"main_file"}],"doi":"10.1016/j.jtbi.2015.07.011","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"pubrep_id":"483","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"publication":"Journal of Theoretical Biology","scopus_import":"1","publisher":"Elsevier","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","ec_funded":1,"fulldoi":"https://doi.org/10.1016/j.jtbi.2015.07.011","volume":383,"page":"28 - 43","oa_version":"Published Version","publication_status":"published","corr_author":"1"},{"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available at: \r\nhttps://repository.ist.ac.at/331/\r\n","related_material":{"record":[{"id":"5415","relation":"earlier_version","status":"public"},{"id":"5436","status":"public","relation":"earlier_version"},{"id":"467","relation":"later_version","status":"public"}]},"doi":"10.1109/LICS.2015.72","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings - Symposium on Logic in Computer Science","article_processing_charge":"No","quality_controlled":"1","type":"conference","fulldoi":"https://doi.org/10.1109/LICS.2015.72","ec_funded":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1606.03598"}],"publisher":"IEEE","oa_version":"Preprint","publication_status":"published","corr_author":"1","volume":"2015-July","article_number":"7174926","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"OA_type":"green","year":"2015","citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174926.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” In <i>Proceedings - Symposium on Logic in Computer Science</i>, Vol. 2015–July. IEEE, 2015. <a href=\"https://doi.org/10.1109/LICS.2015.72\">https://doi.org/10.1109/LICS.2015.72</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in <i>Proceedings - Symposium on Logic in Computer Science</i>, Kyoto, Japan, 2015, vol. 2015–July.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: <i>Proceedings - Symposium on Logic in Computer Science</i>. Vol 2015-July. IEEE; 2015. doi:<a href=\"https://doi.org/10.1109/LICS.2015.72\">10.1109/LICS.2015.72</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2015). Nested weighted automata. In <i>Proceedings - Symposium on Logic in Computer Science</i> (Vol. 2015–July). Kyoto, Japan: IEEE. <a href=\"https://doi.org/10.1109/LICS.2015.72\">https://doi.org/10.1109/LICS.2015.72</a>","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” <i>Proceedings - Symposium on Logic in Computer Science</i>, vol. 2015–July, 7174926, IEEE, 2015, doi:<a href=\"https://doi.org/10.1109/LICS.2015.72\">10.1109/LICS.2015.72</a>."},"date_created":"2018-12-11T11:53:17Z","status":"public","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan"}],"conference":{"name":"LICS: Logic in Computer Science","end_date":"2015-07-10","location":"Kyoto, Japan","start_date":"2015-07-06"},"oa":1,"month":"07","external_id":{"isi":["000380427100064"],"arxiv":["1606.03598"]},"date_published":"2015-07-31T00:00:00Z","date_updated":"2026-07-07T14:01:10Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","isi":1,"day":"31","_id":"1656","language":[{"iso":"eng"}],"publist_id":"5494","arxiv":1,"title":"Nested weighted automata"},{"publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-04-24T00:00:00Z","date_updated":"2026-07-07T14:01:10Z","ddc":["000"],"title":"Nested weighted automata","_id":"5436","language":[{"iso":"eng"}],"day":"24","status":"public","year":"2015","date_created":"2018-12-12T11:39:19Z","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. <i>Nested Weighted Automata</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">10.15479/AT:IST-2015-170-v2-2</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2015). <i>Nested weighted automata</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">https://doi.org/10.15479/AT:IST-2015-170-v2-2</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. <i>Nested Weighted Automata</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">10.15479/AT:IST-2015-170-v2-2</a>.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. <i>Nested Weighted Automata</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-170-v2-2\">https://doi.org/10.15479/AT:IST-2015-170-v2-2</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria, 29p.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, <i>Nested weighted automata</i>. IST Austria, 2015."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"04","has_accepted_license":"1","oa":1,"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"}],"publisher":"IST Austria","type":"technical_report","fulldoi":"https://doi.org/10.15479/AT:IST-2015-170-v2-2","alternative_title":["IST Austria Technical Report"],"page":"29","oa_version":"Published Version","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:54Z","date_created":"2018-12-12T11:54:19Z","relation":"main_file","file_id":"5541","file_name":"IST-2015-170-v2+2_report.pdf","creator":"system","checksum":"3c402f47d3669c28d04d1af405a08e3f","file_size":569991}],"doi":"10.15479/AT:IST-2015-170-v2-2","related_material":{"record":[{"id":"5415","relation":"earlier_version","status":"public"},{"relation":"later_version","status":"public","id":"1656"},{"status":"public","relation":"later_version","id":"467"}]},"pubrep_id":"331","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time.\r\nIn nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}]},{"date_published":"2015-12-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-07-29T10:08:33Z","intvolume":"        31","language":[{"iso":"eng"}],"_id":"1792","day":"01","isi":1,"issue":"6","title":"A Koksma-Hlawka inequality for general discrepancy systems","publist_id":"5320","citation":{"apa":"Pausinger, F., &#38; Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. <i>Journal of Complexity</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">https://doi.org/10.1016/j.jco.2015.06.002</a>","short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. <i>Journal of Complexity</i>. 2015;31(6):773-797. doi:<a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">10.1016/j.jco.2015.06.002</a>","mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” <i>Journal of Complexity</i>, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:<a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">10.1016/j.jco.2015.06.002</a>.","ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” <i>Journal of Complexity</i>, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797.","chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” <i>Journal of Complexity</i>. Academic Press, 2015. <a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">https://doi.org/10.1016/j.jco.2015.06.002</a>."},"date_created":"2018-12-11T11:54:02Z","year":"2015","department":[{"_id":"HeEd"}],"status":"public","author":[{"orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger"},{"last_name":"Svane","first_name":"Anne","full_name":"Svane, Anne"}],"external_id":{"isi":["000362926900001"]},"month":"12","fulldoi":"https://doi.org/10.1016/j.jco.2015.06.002","type":"journal_article","publisher":"Academic Press","scopus_import":"1","corr_author":"1","publication_status":"published","oa_version":"None","page":"773 - 797","volume":31,"doi":"10.1016/j.jco.2015.06.002","related_material":{"record":[{"id":"1399","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","publication":"Journal of Complexity","abstract":[{"text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No"},{"page":"144","doi_confirm":"1","alternative_title":["ISTA Thesis"],"title":"On the approximation of intrinsic volumes","publist_id":"5808","corr_author":"1","_id":"1399","language":[{"iso":"eng"}],"day":"01","publication_status":"published","oa_version":"None","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"date_published":"2015-06-01T00:00:00Z","date_updated":"2026-07-29T10:08:34Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","month":"06","article_processing_charge":"No","degree_awarded":"PhD","author":[{"full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"}],"abstract":[{"text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold.","lang":"eng"}],"status":"public","citation":{"chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","apa":"Pausinger, F. (2015). <i>On the approximation of intrinsic volumes</i>. Institute of Science and Technology Austria.","mla":"Pausinger, Florian. <i>On the Approximation of Intrinsic Volumes</i>. Institute of Science and Technology Austria, 2015."},"date_created":"2018-12-11T11:51:48Z","supervisor":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"year":"2015","related_material":{"record":[{"id":"1662","relation":"part_of_dissertation","status":"public"},{"id":"1792","relation":"part_of_dissertation","status":"public"},{"id":"2255","status":"public","relation":"part_of_dissertation"}]},"department":[{"_id":"HeEd"},{"_id":"GradSch"}]},{"title":"Biological auctions with multiple rewards","publist_id":"5425","_id":"1709","language":[{"iso":"eng"}],"issue":"1812","isi":1,"pmid":1,"day":"15","intvolume":"       282","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-07-15T00:00:00Z","date_updated":"2026-07-29T10:15:25Z","external_id":{"pmid":["26180069"],"isi":["000362305500021"]},"month":"07","oa":1,"author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"},{"last_name":"Gupta","first_name":"Raghav","full_name":"Gupta, Raghav"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"status":"public","year":"2015","date_created":"2018-12-11T11:53:35Z","citation":{"short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., &#38; Chatterjee, K. (2015). Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>","ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1812). doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>","mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>.","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812. Royal Society, 2015.","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>.","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812)."},"department":[{"_id":"KrCh"}],"volume":282,"corr_author":"1","oa_version":"Submitted Version","publication_status":"published","publisher":"Royal Society","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/"}],"type":"journal_article","fulldoi":"https://doi.org/10.1098/rspb.2015.1041","quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","article_type":"original","abstract":[{"text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards.","lang":"eng"}],"doi":"10.1098/rspb.2015.1041","related_material":{"record":[{"id":"1400","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award."},{"degree_awarded":"PhD","author":[{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"}],"abstract":[{"text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease.","lang":"eng"}],"month":"04","article_processing_charge":"No","year":"2015","supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"date_created":"2018-12-11T11:51:48Z","citation":{"short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015.","apa":"Reiter, J. (2015). <i>The subclonal evolution of cancer</i>. Institute of Science and Technology Austria.","ama":"Reiter J. The subclonal evolution of cancer. 2015.","mla":"Reiter, Johannes. <i>The Subclonal Evolution of Cancer</i>. Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015."},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"related_material":{"record":[{"id":"2000","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1709"},{"id":"2858","status":"public","relation":"part_of_dissertation"},{"id":"2816","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2247"},{"id":"3260","status":"public","relation":"part_of_dissertation"},{"id":"3157","relation":"part_of_dissertation","status":"public"}]},"status":"public","corr_author":"1","_id":"1400","language":[{"iso":"eng"}],"oa_version":"None","day":"01","publication_status":"published","title":"The subclonal evolution of cancer","alternative_title":["ISTA Thesis"],"page":"183","doi_confirm":"1","publist_id":"5807","date_published":"2015-04-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-07-29T10:15:25Z","type":"dissertation","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]}},{"scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Public Library of Science","fulldoi":"https://doi.org/10.1371/journal.pgen.1005639","ec_funded":1,"type":"journal_article","volume":11,"publication_status":"published","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:07:58Z","content_type":"application/pdf","access_level":"open_access","file_size":2580778,"checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","creator":"system","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","file_id":"4657","relation":"main_file"}],"related_material":{"record":[{"id":"9712","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"1131"}]},"doi":"10.1371/journal.pgen.1005639","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"publication":"PLoS Genetics","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"pubrep_id":"463","file_date_updated":"2020-07-14T12:45:10Z","intvolume":"        11","date_published":"2015-11-06T00:00:00Z","date_updated":"2026-07-29T11:31:13Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["576"],"publist_id":"5483","title":"Dynamics of transcription factor binding site evolution","day":"06","isi":1,"issue":"11","_id":"1666","language":[{"iso":"eng"}],"status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"date_created":"2018-12-11T11:53:21Z","citation":{"mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>.","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015."},"year":"2015","month":"11","external_id":{"isi":["000366179000022"]},"author":[{"last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"}],"has_accepted_license":"1","oa":1},{"article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix."}],"project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"pubrep_id":"609","file":[{"file_id":"5131","creator":"system","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","checksum":"955aee971983f6b6152bcc1c9b4a7c20","file_size":20154270,"relation":"main_file","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:15:13Z","access_level":"open_access","content_type":"application/pdf"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"839"}]},"doi":"10.1145/2766896","article_number":"151","volume":34,"publication_status":"published","oa_version":"Submitted Version","corr_author":"1","scopus_import":"1","publisher":"ACM","ec_funded":1,"fulldoi":"https://doi.org/10.1145/2766896","type":"conference","month":"07","external_id":{"isi":["000358786600117"]},"conference":{"start_date":"2015-08-09","location":"Los Angeles, CA, United States","end_date":"2015-08-13","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"author":[{"full_name":"Hahn, David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","last_name":"Hahn","first_name":"David"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"oa":1,"has_accepted_license":"1","status":"public","department":[{"_id":"ChWo"}],"citation":{"ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. <a href=\"https://doi.org/10.1145/2766896\">https://doi.org/10.1145/2766896</a>.","ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151.","apa":"Hahn, D., &#38; Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2766896\">https://doi.org/10.1145/2766896</a>","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:<a href=\"https://doi.org/10.1145/2766896\">10.1145/2766896</a>","mla":"Hahn, David, and Chris Wojtan. <i>High-Resolution Brittle Fracture Simulation with Boundary Elements</i>. Vol. 34, no. 4, 151, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2766896\">10.1145/2766896</a>."},"date_created":"2018-12-11T11:53:09Z","year":"2015","publist_id":"5522","title":"High-resolution brittle fracture simulation with boundary elements","day":"27","isi":1,"issue":"4","_id":"1633","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:07Z","intvolume":"        34","date_published":"2015-07-27T00:00:00Z","date_updated":"2026-07-29T13:27:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"]},{"pmid":1,"issue":"1669","isi":1,"day":"26","_id":"1830","language":[{"iso":"eng"}],"publist_id":"5273","title":"Opposing effects of allogrooming on disease transmission in ant societies","date_updated":"2026-08-12T06:27:32Z","date_published":"2015-05-26T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       370","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"author":[{"full_name":"Theis, Fabian","first_name":"Fabian","last_name":"Theis"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"last_name":"Marr","first_name":"Carsten","full_name":"Marr, Carsten"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"oa":1,"month":"05","external_id":{"isi":["000354143400010"],"pmid":["25870394"]},"department":[{"_id":"SyCr"}],"year":"2015","citation":{"short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","apa":"Theis, F., Ugelvig, L. V., Marr, C., &#38; Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2014.0108\">https://doi.org/10.1098/rstb.2014.0108</a>","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2015;370(1669). doi:<a href=\"https://doi.org/10.1098/rstb.2014.0108\">10.1098/rstb.2014.0108</a>","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rstb.2014.0108\">10.1098/rstb.2014.0108</a>.","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669. Royal Society, 2015.","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rstb.2014.0108\">https://doi.org/10.1098/rstb.2014.0108</a>.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669)."},"date_created":"2018-12-11T11:54:15Z","status":"public","oa_version":"Submitted Version","publication_status":"published","corr_author":"1","volume":370,"type":"journal_article","fulldoi":"https://doi.org/10.1098/rstb.2014.0108","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/"}],"scopus_import":"1","publisher":"Royal Society","abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"article_type":"original","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","call_identifier":"FP7"},{"call_identifier":"FP7","grant_number":"302004","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425"},{"_id":"25E0E184-B435-11E9-9278-68D0E5697425","name":"Schnellboot Antnet Junge Akademie"},{"_id":"25E24DB2-B435-11E9-9278-68D0E5697425","name":"Fellowship of Wissenschaftskolleg zu Berlin"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","article_processing_charge":"No","quality_controlled":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"9721"}]},"acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","doi":"10.1098/rstb.2014.0108"},{"oa_version":"Published Version","day":"29","_id":"9721","title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","type":"research_data_reference","fulldoi":"https://doi.org/10.5061/dryad.dj2bf","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2026-08-12T06:27:32Z","date_published":"2015-12-29T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.dj2bf"}],"publisher":"Dryad","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"author":[{"full_name":"Theis, Fabian","first_name":"Fabian","last_name":"Theis"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883"},{"full_name":"Marr, Carsten","last_name":"Marr","first_name":"Carsten"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"oa":1,"month":"12","article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1830"}]},"department":[{"_id":"SyCr"}],"year":"2015","citation":{"mla":"Theis, Fabian, et al. <i>Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","apa":"Theis, F., Ugelvig, L. V., Marr, C., &#38; Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. <a href=\"https://doi.org/10.5061/dryad.dj2bf\">https://doi.org/10.5061/dryad.dj2bf</a>","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.dj2bf\">https://doi.org/10.5061/dryad.dj2bf</a>.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, <a href=\"https://doi.org/10.5061/dryad.dj2bf\">10.5061/dryad.dj2bf</a>."},"doi":"10.5061/dryad.dj2bf","date_created":"2021-07-26T09:38:36Z","status":"public"},{"author":[{"full_name":"Safari, Laleh","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari"},{"full_name":"Santos, José","first_name":"José","last_name":"Santos"},{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"full_name":"Jänkälä, Kari","first_name":"Kari","last_name":"Jänkälä"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"}],"oa":1,"month":"05","external_id":{"isi":["000355920800016"],"arxiv":["1409.0110"]},"department":[{"_id":"MiLe"}],"date_created":"2018-12-11T11:54:08Z","citation":{"apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, AIP Publishing, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. AIP Publishing, 2015.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>.","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105."},"year":"2015","status":"public","day":"20","issue":"5","isi":1,"_id":"1811","language":[{"iso":"eng"}],"publist_id":"5295","arxiv":1,"title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","date_updated":"2026-08-12T13:58:42Z","date_published":"2015-05-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        56","abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"publication":"Journal of Mathematical Physics","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","doi":"10.1063/1.4921227","publication_status":"published","oa_version":"Preprint","corr_author":"1","article_number":"052105","volume":56,"fulldoi":"https://doi.org/10.1063/1.4921227","ec_funded":1,"type":"journal_article","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"publisher":"AIP Publishing"},{"department":[{"_id":"LaEr"}],"citation":{"ieee":"J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 10. AIP Publishing, 2015.","chicago":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2015. <a href=\"https://doi.org/10.1063/1.4932606\">https://doi.org/10.1063/1.4932606</a>.","ista":"Alt J. 2015. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 56(10), 103301.","mla":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 10, 103301, AIP Publishing, 2015, doi:<a href=\"https://doi.org/10.1063/1.4932606\">10.1063/1.4932606</a>.","apa":"Alt, J. (2015). The local semicircle law for random matrices with a fourfold symmetry. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4932606\">https://doi.org/10.1063/1.4932606</a>","short":"J. Alt, Journal of Mathematical Physics 56 (2015).","ama":"Alt J. The local semicircle law for random matrices with a fourfold symmetry. <i>Journal of Mathematical Physics</i>. 2015;56(10). doi:<a href=\"https://doi.org/10.1063/1.4932606\">10.1063/1.4932606</a>"},"date_created":"2018-12-11T11:53:25Z","year":"2015","status":"public","author":[{"last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes"}],"oa":1,"month":"10","external_id":{"isi":["000364237000026"],"arxiv":["1506.04683"]},"date_updated":"2026-08-12T13:58:57Z","date_published":"2015-10-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        56","day":"09","issue":"10","isi":1,"language":[{"iso":"eng"}],"_id":"1677","arxiv":1,"publist_id":"5472","title":"The local semicircle law for random matrices with a fourfold symmetry","related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"doi":"10.1063/1.4932606","abstract":[{"text":"We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale.","lang":"eng"}],"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"publication":"Journal of Mathematical Physics","article_processing_charge":"No","quality_controlled":"1","ec_funded":1,"fulldoi":"https://doi.org/10.1063/1.4932606","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.04683"}],"scopus_import":"1","publisher":"AIP Publishing","publication_status":"published","oa_version":"Preprint","corr_author":"1","article_number":"103301","volume":56},{"month":"12","external_id":{"isi":["000367373900002"],"arxiv":["1511.03585"]},"author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh"},{"first_name":"Aldo","last_name":"Antognini","full_name":"Antognini, Aldo"},{"full_name":"Indelicato, Paul","last_name":"Indelicato","first_name":"Paul"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"}],"oa":1,"status":"public","department":[{"_id":"MiLe"}],"citation":{"apa":"Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., &#38; Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">https://doi.org/10.1103/PhysRevA.92.062506</a>","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015).","ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. <i>Physical Review A</i>. 2015;92(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">10.1103/PhysRevA.92.062506</a>","mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” <i>Physical Review A</i>, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">10.1103/PhysRevA.92.062506</a>.","ieee":"P. Amaro <i>et al.</i>, “Quantum interference shifts in laser spectroscopy with elliptical polarization,” <i>Physical Review A</i>, vol. 92, no. 6. American Physical Society, 2015.","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” <i>Physical Review A</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">https://doi.org/10.1103/PhysRevA.92.062506</a>.","ista":"Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A. 92(6), 062506."},"date_created":"2018-12-11T11:52:53Z","year":"2015","publist_id":"5584","arxiv":1,"title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","day":"31","isi":1,"issue":"6","_id":"1587","language":[{"iso":"eng"}],"intvolume":"        92","date_updated":"2026-08-12T14:20:30Z","date_published":"2015-12-31T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme."}],"article_type":"original","publication":"Physical Review A","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.1103/PhysRevA.92.062506","article_number":"062506","volume":92,"publication_status":"published","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03585"}],"publisher":"American Physical Society","ec_funded":1,"fulldoi":"https://doi.org/10.1103/PhysRevA.92.062506","type":"journal_article"},{"issue":"6","isi":1,"day":"15","_id":"1940","language":[{"iso":"eng"}],"publist_id":"5145","arxiv":1,"title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","date_updated":"2026-08-12T14:28:08Z","date_published":"2015-06-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        91","author":[{"full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"oa":1,"month":"06","external_id":{"arxiv":["1501.04015"],"isi":["000356131600006"]},"department":[{"_id":"GaTk"}],"year":"2015","date_created":"2018-12-11T11:54:49Z","citation":{"mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” <i>Physical Review E</i>, vol. 91, no. 6, 062710, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">10.1103/PhysRevE.91.062710</a>.","ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. <i>Physical Review E</i>. 2015;91(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">10.1103/PhysRevE.91.062710</a>","apa":"Sokolowski, T. R., &#38; Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">https://doi.org/10.1103/PhysRevE.91.062710</a>","short":"T.R. Sokolowski, G. Tkačik, Physical Review E 91 (2015).","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” <i>Physical Review E</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">https://doi.org/10.1103/PhysRevE.91.062710</a>.","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E. 91(6), 062710.","ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” <i>Physical Review E</i>, vol. 91, no. 6. American Physical Society, 2015."},"status":"public","oa_version":"Preprint","publication_status":"published","corr_author":"1","volume":91,"article_number":"062710","type":"journal_article","fulldoi":"https://doi.org/10.1103/PhysRevE.91.062710","main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"scopus_import":"1","publisher":"American Physical Society","abstract":[{"text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the &quot;input&quot;) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.","lang":"eng"}],"publication":"Physical Review E","article_processing_charge":"No","quality_controlled":"1","doi":"10.1103/PhysRevE.91.062710"},{"oa_version":"Preprint","publication_status":"published","volume":91,"article_number":"022803","type":"journal_article","fulldoi":"https://doi.org/10.1103/PhysRevE.91.022803","publisher":"American Physical Society","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1012.3298","open_access":"1"}],"publication":"Physical Review E","article_type":"original","abstract":[{"lang":"eng","text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1103/PhysRevE.91.022803","_id":"1883","language":[{"iso":"eng"}],"issue":"2","isi":1,"day":"02","title":"Anomalous scaling in an age-dependent branching model","arxiv":1,"publist_id":"5213","date_updated":"2026-08-12T14:26:46Z","date_published":"2015-02-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        91","oa":1,"author":[{"first_name":"Stephanie","last_name":"Keller-Schmidt","full_name":"Keller-Schmidt, Stephanie"},{"first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat"},{"full_name":"Eguíluz, Víctor","last_name":"Eguíluz","first_name":"Víctor"},{"last_name":"Hernandez Garcia","first_name":"Emilio","full_name":"Hernandez Garcia, Emilio"},{"full_name":"Klemm, Konstantin","first_name":"Konstantin","last_name":"Klemm"}],"external_id":{"isi":["000349860900006"],"arxiv":["1012.3298"]},"month":"02","year":"2015","date_created":"2018-12-11T11:54:31Z","citation":{"mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E</i>, vol. 91, no. 2, 022803, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E 91 (2015).","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., &#38; Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. <i>Physical Review E</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” <i>Physical Review E</i>, vol. 91, no. 2. American Physical Society, 2015.","ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E. 91(2), 022803.","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>."},"department":[{"_id":"NiBa"}],"status":"public"},{"page":"3496-3502","volume":5,"alternative_title":["Artifical Intelligence"],"corr_author":"1","publication_status":"published","oa_version":"Preprint","publisher":"AAAI Press","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"ec_funded":1,"fulldoi":"https://doi.org/10.1609/aaai.v29i1.9683","type":"conference","quality_controlled":"1","article_processing_charge":"No","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.","lang":"eng"}],"doi":"10.1609/aaai.v29i1.9683","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","related_material":{"record":[{"id":"1529","status":"public","relation":"later_version"}]},"title":"Optimal cost almost-sure reachability in POMDPs","arxiv":1,"publist_id":"5286","_id":"1820","language":[{"iso":"eng"}],"day":"01","isi":1,"intvolume":"         5","date_published":"2015-06-01T00:00:00Z","date_updated":"2026-08-19T09:31:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000372683700002"],"arxiv":["1411.3880"]},"month":"06","oa":1,"conference":{"start_date":"2015-01-25","location":"Austin, TX, USA","end_date":"2015-01-30","name":"IAAI: Innovative Applications of Artificial Intelligence"},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","first_name":"Raghav","last_name":"Gupta"},{"full_name":"Kanodia, Ayush","last_name":"Kanodia","first_name":"Ayush"}],"status":"public","date_created":"2018-12-11T11:54:11Z","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, vol. 5, AAAI Press, 2015, pp. 3496–502, doi:<a href=\"https://doi.org/10.1609/aaai.v29i1.9683\">10.1609/aaai.v29i1.9683</a>.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>. Vol 5. AAAI Press; 2015:3496-3502. doi:<a href=\"https://doi.org/10.1609/aaai.v29i1.9683\">10.1609/aaai.v29i1.9683</a>","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i> (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v29i1.9683\">https://doi.org/10.1609/aaai.v29i1.9683</a>","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, 5:3496–3502. AAAI Press, 2015. <a href=\"https://doi.org/10.1609/aaai.v29i1.9683\">https://doi.org/10.1609/aaai.v29i1.9683</a>.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, Austin, TX, USA, 2015, vol. 5, pp. 3496–3502."},"year":"2015","department":[{"_id":"KrCh"}]}]