[{"file":[{"file_size":2580778,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:10Z","date_created":"2018-12-12T10:07:58Z","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","relation":"main_file","creator":"system","file_id":"4657","access_level":"open_access"}],"scopus_import":"1","publisher":"Public Library of Science","author":[{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","first_name":"Murat"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455"}],"title":"Dynamics of transcription factor binding site evolution","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:10Z","_id":"1666","date_created":"2018-12-11T11:53:21Z","language":[{"iso":"eng"}],"year":"2015","intvolume":" 11","oa":1,"volume":11,"publication":"PLoS Genetics","day":"06","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"id":"9712","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"1131"}]},"month":"11","type":"journal_article","external_id":{"isi":["000366179000022"]},"oa_version":"Published Version","publist_id":"5483","citation":{"ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639"},"ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2015-11-06T00:00:00Z","isi":1,"doi":"10.1371/journal.pgen.1005639","status":"public","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","has_accepted_license":"1","pubrep_id":"463","publication_status":"published","issue":"11","fulldoi":"https://doi.org/10.1371/journal.pgen.1005639","date_updated":"2026-07-29T11:31:13Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1},{"day":"27","volume":34,"intvolume":" 34","conference":{"end_date":"2015-08-13","start_date":"2015-08-09","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, United States"},"oa":1,"corr_author":"1","language":[{"iso":"eng"}],"year":"2015","file_date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-11T11:53:09Z","_id":"1633","author":[{"id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David","last_name":"Hahn","first_name":"David"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"title":"High-resolution brittle fracture simulation with boundary elements","quality_controlled":"1","file":[{"file_size":20154270,"content_type":"application/pdf","date_created":"2018-12-12T10:15:13Z","date_updated":"2020-07-14T12:45:07Z","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","relation":"main_file","creator":"system","file_id":"5131","access_level":"open_access","checksum":"955aee971983f6b6152bcc1c9b4a7c20"}],"scopus_import":"1","publisher":"ACM","issue":"4","pubrep_id":"609","publication_status":"published","fulldoi":"https://doi.org/10.1145/2766896","date_updated":"2026-07-29T13:27:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"department":[{"_id":"ChWo"}],"article_processing_charge":"No","has_accepted_license":"1","article_number":"151","doi":"10.1145/2766896","isi":1,"project":[{"grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"status":"public","citation":{"ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.","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.","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.","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","apa":"Hahn, D., & 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. https://doi.org/10.1145/2766896","mla":"Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896."},"ddc":["000"],"date_published":"2015-07-27T00:00:00Z","type":"conference","external_id":{"isi":["000358786600117"]},"oa_version":"Submitted Version","publist_id":"5522","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"839"}]},"month":"07"},{"issue":"1669","publication_status":"published","fulldoi":"https://doi.org/10.1098/rstb.2014.0108","date_updated":"2026-08-12T06:27:32Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"SyCr"}],"article_processing_charge":"No","citation":{"chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0108.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0108","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).","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, 2015.","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, Royal Society, 2015, doi:10.1098/rstb.2014.0108.","apa":"Theis, F., Ugelvig, L. V., 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. Royal Society. https://doi.org/10.1098/rstb.2014.0108"},"date_published":"2015-05-26T00:00:00Z","doi":"10.1098/rstb.2014.0108","isi":1,"status":"public","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004","call_identifier":"FP7","_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"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/"}],"related_material":{"record":[{"relation":"research_data","id":"9721","status":"public"}]},"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"}],"month":"05","type":"journal_article","external_id":{"isi":["000354143400010"],"pmid":["25870394"]},"oa_version":"Submitted Version","publist_id":"5273","volume":370,"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","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.","day":"26","corr_author":"1","language":[{"iso":"eng"}],"year":"2015","intvolume":" 370","oa":1,"date_created":"2018-12-11T11:54:15Z","_id":"1830","scopus_import":"1","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"publisher":"Royal Society","author":[{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","full_name":"Ugelvig, Line V"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"article_type":"original","title":"Opposing effects of allogrooming on disease transmission in ant societies","quality_controlled":"1"},{"department":[{"_id":"SyCr"}],"article_processing_charge":"No","oa":1,"year":"2015","day":"29","date_updated":"2026-08-12T06:27:32Z","fulldoi":"https://doi.org/10.5061/dryad.dj2bf","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","author":[{"first_name":"Fabian","last_name":"Theis","full_name":"Theis, Fabian"},{"orcid":"0000-0003-1832-8883","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","last_name":"Ugelvig"},{"last_name":"Marr","full_name":"Marr, Carsten","first_name":"Carsten"},{"first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1830"}]},"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."}],"month":"12","publisher":"Dryad","doi":"10.5061/dryad.dj2bf","status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.dj2bf","open_access":"1"}],"citation":{"ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf","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. https://doi.org/10.5061/dryad.dj2bf.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","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.","mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf"},"_id":"9721","date_created":"2021-07-26T09:38:36Z","date_published":"2015-12-29T00:00:00Z"},{"title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","author":[{"last_name":"Safari","full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"},{"first_name":"Pedro","full_name":"Amaro, Pedro","last_name":"Amaro"},{"first_name":"Kari","full_name":"Jänkälä, Kari","last_name":"Jänkälä"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"}],"publisher":"AIP Publishing","scopus_import":"1","date_created":"2018-12-11T11:54:08Z","_id":"1811","oa":1,"intvolume":" 56","year":"2015","language":[{"iso":"eng"}],"corr_author":"1","day":"20","arxiv":1,"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.","publication":"Journal of Mathematical Physics","volume":56,"publist_id":"5295","oa_version":"Preprint","external_id":{"arxiv":["1409.0110"],"isi":["000355920800016"]},"type":"journal_article","month":"05","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"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"status":"public","doi":"10.1063/1.4921227","isi":1,"date_published":"2015-05-20T00:00:00Z","citation":{"apa":"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. AIP Publishing. https://doi.org/10.1063/1.4921227","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics, vol. 56, no. 5, 052105, AIP Publishing, 2015, doi:10.1063/1.4921227.","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” Journal of Mathematical Physics, vol. 56, no. 5. AIP Publishing, 2015.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics. AIP Publishing, 2015. https://doi.org/10.1063/1.4921227.","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 2015;56(5). doi:10.1063/1.4921227","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."},"article_processing_charge":"No","department":[{"_id":"MiLe"}],"article_number":"052105","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"fulldoi":"https://doi.org/10.1063/1.4921227","date_updated":"2026-08-12T13:58:42Z","issue":"5","publication_status":"published"},{"year":"2015","corr_author":"1","language":[{"iso":"eng"}],"oa":1,"intvolume":" 56","publication":"Journal of Mathematical Physics","volume":56,"arxiv":1,"day":"09","publisher":"AIP Publishing","scopus_import":"1","title":"The local semicircle law for random matrices with a fourfold symmetry","quality_controlled":"1","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes"}],"date_created":"2018-12-11T11:53:25Z","_id":"1677","article_number":"103301","article_processing_charge":"No","department":[{"_id":"LaEr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"publication_status":"published","issue":"10","date_updated":"2026-08-12T13:58:57Z","fulldoi":"https://doi.org/10.1063/1.4932606","month":"10","related_material":{"record":[{"relation":"dissertation_contains","id":"149","status":"public"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","publist_id":"5472","external_id":{"isi":["000364237000026"],"arxiv":["1506.04683"]},"type":"journal_article","date_published":"2015-10-09T00:00:00Z","citation":{"mla":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics, vol. 56, no. 10, 103301, AIP Publishing, 2015, doi:10.1063/1.4932606.","apa":"Alt, J. (2015). The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4932606","ama":"Alt J. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 2015;56(10). doi:10.1063/1.4932606","ista":"Alt J. 2015. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 56(10), 103301.","chicago":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics. AIP Publishing, 2015. https://doi.org/10.1063/1.4932606.","short":"J. Alt, Journal of Mathematical Physics 56 (2015).","ieee":"J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,” Journal of Mathematical Physics, vol. 56, no. 10. AIP Publishing, 2015."},"status":"public","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.04683"}],"doi":"10.1063/1.4932606","isi":1},{"publisher":"American Physical Society","scopus_import":"1","title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","quality_controlled":"1","article_type":"original","author":[{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"last_name":"Fratini","full_name":"Fratini, Filippo","first_name":"Filippo"},{"last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh","first_name":"Laleh"},{"full_name":"Antognini, Aldo","last_name":"Antognini","first_name":"Aldo"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"first_name":"Randolf","last_name":"Pohl","full_name":"Pohl, Randolf"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"date_created":"2018-12-11T11:52:53Z","_id":"1587","year":"2015","language":[{"iso":"eng"}],"oa":1,"intvolume":" 92","volume":92,"publication":"Physical Review A","day":"31","arxiv":1,"month":"12","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","publist_id":"5584","type":"journal_article","external_id":{"arxiv":["1511.03585"],"isi":["000367373900002"]},"date_published":"2015-12-31T00:00:00Z","citation":{"mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506.","apa":"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. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506","ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A. 2015;92(6). doi:10.1103/PhysRevA.92.062506","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.","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.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506.","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015).","ieee":"P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A, vol. 92, no. 6. American Physical Society, 2015."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03585"}],"isi":1,"doi":"10.1103/PhysRevA.92.062506","article_number":"062506","article_processing_charge":"No","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"issue":"6","publication_status":"published","fulldoi":"https://doi.org/10.1103/PhysRevA.92.062506","date_updated":"2026-08-12T14:20:30Z"},{"arxiv":1,"day":"15","publication":"Physical Review E","volume":91,"intvolume":" 91","oa":1,"corr_author":"1","language":[{"iso":"eng"}],"year":"2015","date_created":"2018-12-11T11:54:49Z","_id":"1940","author":[{"full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","first_name":"Thomas R","orcid":"0000-0002-1287-3779"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","quality_controlled":"1","scopus_import":"1","publisher":"American Physical Society","issue":"6","publication_status":"published","date_updated":"2026-08-12T14:28:08Z","fulldoi":"https://doi.org/10.1103/PhysRevE.91.062710","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"article_processing_charge":"No","article_number":"062710","isi":1,"doi":"10.1103/PhysRevE.91.062710","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"citation":{"ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E, vol. 91, no. 6. American Physical Society, 2015.","short":"T.R. Sokolowski, G. Tkačik, Physical Review E 91 (2015).","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E. 91(6), 062710.","ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E. 2015;91(6). doi:10.1103/PhysRevE.91.062710","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.91.062710.","apa":"Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.91.062710","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E, vol. 91, no. 6, 062710, American Physical Society, 2015, doi:10.1103/PhysRevE.91.062710."},"date_published":"2015-06-15T00:00:00Z","type":"journal_article","external_id":{"arxiv":["1501.04015"],"isi":["000356131600006"]},"oa_version":"Preprint","publist_id":"5145","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 "input") 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"}],"month":"06"},{"date_created":"2018-12-11T11:54:31Z","_id":"1883","title":"Anomalous scaling in an age-dependent branching model","quality_controlled":"1","article_type":"original","author":[{"first_name":"Stephanie","last_name":"Keller-Schmidt","full_name":"Keller-Schmidt, Stephanie"},{"first_name":"Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"},{"first_name":"Víctor","last_name":"Eguíluz","full_name":"Eguíluz, Víctor"},{"last_name":"Hernandez Garcia","full_name":"Hernandez Garcia, Emilio","first_name":"Emilio"},{"first_name":"Konstantin","full_name":"Klemm, Konstantin","last_name":"Klemm"}],"publisher":"American Physical Society","scopus_import":"1","arxiv":1,"day":"02","volume":91,"publication":"Physical Review E","oa":1,"intvolume":" 91","year":"2015","language":[{"iso":"eng"}],"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1012.3298","open_access":"1"}],"isi":1,"doi":"10.1103/PhysRevE.91.022803","date_published":"2015-02-02T00:00:00Z","citation":{"apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.91.022803","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E, vol. 91, no. 2, 022803, American Physical Society, 2015, doi:10.1103/PhysRevE.91.022803.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E 91 (2015).","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E, 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.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.91.022803.","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E. 2015;91(2). doi:10.1103/PhysRevE.91.022803"},"oa_version":"Preprint","publist_id":"5213","external_id":{"arxiv":["1012.3298"],"isi":["000349860900006"]},"type":"journal_article","month":"02","abstract":[{"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","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","issue":"2","fulldoi":"https://doi.org/10.1103/PhysRevE.91.022803","date_updated":"2026-08-12T14:26:46Z","article_processing_charge":"No","department":[{"_id":"NiBa"}],"article_number":"022803"},{"article_processing_charge":"No","department":[{"_id":"KrCh"}],"alternative_title":["Artifical Intelligence"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"date_updated":"2026-08-19T09:31:47Z","fulldoi":"https://doi.org/10.1609/aaai.v29i1.9683","publication_status":"published","publist_id":"5286","oa_version":"Preprint","external_id":{"arxiv":["1411.3880"],"isi":["000372683700002"]},"type":"conference","month":"06","related_material":{"record":[{"status":"public","id":"1529","relation":"later_version"}]},"abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"status":"public","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"doi":"10.1609/aaai.v29i1.9683","isi":1,"date_published":"2015-06-01T00:00:00Z","citation":{"ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502. doi:10.1609/aaai.v29i1.9683","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015. https://doi.org/10.1609/aaai.v29i1.9683.","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 Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","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.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press. https://doi.org/10.1609/aaai.v29i1.9683","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502, doi:10.1609/aaai.v29i1.9683."},"oa":1,"conference":{"end_date":"2015-01-30","start_date":"2015-01-25","name":"IAAI: Innovative Applications of Artificial Intelligence","location":"Austin, TX, USA"},"intvolume":" 5","year":"2015","language":[{"iso":"eng"}],"corr_author":"1","arxiv":1,"day":"01","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.","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","volume":5,"quality_controlled":"1","title":"Optimal cost almost-sure reachability in POMDPs","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"}],"publisher":"AAAI Press","scopus_import":"1","date_created":"2018-12-11T11:54:11Z","_id":"1820","page":"3496-3502"},{"day":"18","volume":13,"publication":"PLoS Biology","oa":1,"intvolume":" 13","year":"2015","corr_author":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-11T11:53:04Z","_id":"1619","title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","quality_controlled":"1","author":[{"last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume"},{"last_name":"Dravecka","full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","orcid":"0000-0002-2519-8004"},{"first_name":"Tugce","full_name":"Batur, Tugce","last_name":"Batur"},{"full_name":"Guvenek, Aysegul","last_name":"Guvenek","first_name":"Aysegul"},{"first_name":"Dilay","full_name":"Ayhan, Dilay","last_name":"Ayhan"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"publisher":"Public Library of Science","file":[{"checksum":"0e82e3279f50b15c6c170c042627802b","file_id":"4723","access_level":"open_access","creator":"system","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:09:00Z","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","file_size":1387760}],"scopus_import":"1","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"11","publication_status":"published","pubrep_id":"468","fulldoi":"https://doi.org/10.1371/journal.pbio.1002299","date_updated":"2026-10-24T22:31:46Z","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"ToBo"}],"article_number":"e1002299","status":"public","project":[{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"isi":1,"doi":"10.1371/journal.pbio.1002299","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2015-11-18T00:00:00Z","citation":{"apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","ieee":"G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299."},"ddc":["570"],"oa_version":"Published Version","publist_id":"5547","type":"journal_article","external_id":{"isi":["000365898900011"]},"month":"11","abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9711"},{"id":"9765","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"6263"}]}},{"doi":"10.1007/978-3-319-04099-8_9","status":"public","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"citation":{"mla":"Günther, David, et al. “Notes on the Simplification of the Morse-Smale Complex.” Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer et al., Springer Nature, 2014, pp. 135–50, doi:10.1007/978-3-319-04099-8_9.","apa":"Günther, D., Reininghaus, J., Seidel, H.-P., & Weinkauf, T. (2014). Notes on the simplification of the Morse-Smale complex. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III. (pp. 135–150). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-04099-8_9","ama":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. Notes on the simplification of the Morse-Smale complex. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Cham: Springer Nature; 2014:135-150. doi:10.1007/978-3-319-04099-8_9","chicago":"Günther, David, Jan Reininghaus, Hans-Peter Seidel, and Tino Weinkauf. “Notes on the Simplification of the Morse-Smale Complex.” In Topological Methods in Data Analysis and Visualization III., edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 135–50. Mathematics and Visualization. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-319-04099-8_9.","ista":"Günther D, Reininghaus J, Seidel H-P, Weinkauf T. 2014.Notes on the simplification of the Morse-Smale complex. In: Topological Methods in Data Analysis and Visualization III. , 135–150.","ieee":"D. Günther, J. Reininghaus, H.-P. Seidel, and T. Weinkauf, “Notes on the simplification of the Morse-Smale complex,” in Topological Methods in Data Analysis and Visualization III., P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer Nature, 2014, pp. 135–150.","short":"D. Günther, J. Reininghaus, H.-P. Seidel, T. Weinkauf, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III., Springer Nature, Cham, 2014, pp. 135–150."},"date_published":"2014-03-19T00:00:00Z","type":"book_chapter","oa_version":"None","abstract":[{"lang":"eng","text":"The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption."}],"month":"03","date_updated":"2025-04-15T08:37:54Z","fulldoi":"https://doi.org/10.1007/978-3-319-04099-8_9","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"department":[{"_id":"HeEd"}],"article_processing_charge":"No","page":"135-150","_id":"10817","date_created":"2022-03-04T08:33:57Z","author":[{"first_name":"David","last_name":"Günther","full_name":"Günther, David"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan"},{"last_name":"Seidel","full_name":"Seidel, Hans-Peter","first_name":"Hans-Peter"},{"last_name":"Weinkauf","full_name":"Weinkauf, Tino","first_name":"Tino"}],"quality_controlled":"1","title":"Notes on the simplification of the Morse-Smale complex","scopus_import":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["2197-666X"],"eisbn":["9783319040998"],"issn":["1612-3786"],"isbn":["9783319040981"]},"day":"19","acknowledgement":"This research is supported and funded by the Digiteo unTopoVis project, the TOPOSYS project FP7-ICT-318493-STREP, and MPC-VCC.","series_title":"Mathematics and Visualization","publication":"Topological Methods in Data Analysis and Visualization III.","editor":[{"first_name":"Peer-Timo","last_name":"Bremer","full_name":"Bremer, Peer-Timo"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"}],"language":[{"iso":"eng"}],"place":"Cham","year":"2014"},{"intvolume":" 8318","oa":1,"conference":{"end_date":"2014-01-21","start_date":"2014-01-19","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","location":"San Diego, CA, United States"},"language":[{"iso":"eng"}],"year":"2014","arxiv":1,"day":"30","acknowledgement":"This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005.","publication":"Verification, Model Checking, and Abstract Interpretation","volume":8318,"author":[{"first_name":"Benjamin","last_name":"Aminof","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin"},{"last_name":"Jacobs","full_name":"Jacobs, Swen","first_name":"Swen"},{"full_name":"Khalimov, Ayrat","last_name":"Khalimov","first_name":"Ayrat"},{"last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","full_name":"Rubin, Sasha","first_name":"Sasha"}],"quality_controlled":"1","title":"Parameterized model checking of token-passing systems","scopus_import":"1","publisher":"Springer Nature","publication_identifier":{"isbn":["9783642540127"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783642540134"]},"_id":"10884","date_created":"2022-03-18T13:01:22Z","page":"262-281","alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/978-3-642-54013-4_15","date_updated":"2025-04-15T06:29:59Z","publication_status":"published","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1311.4425"]},"type":"conference","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token."}],"month":"01","doi":"10.1007/978-3-642-54013-4_15","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1311.4425"}],"status":"public","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281.","short":"B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281.","ista":"Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.","ama":"Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15","chicago":"Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15.","apa":"Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15."},"date_published":"2014-01-30T00:00:00Z"},{"year":"2014","language":[{"iso":"eng"}],"OA_place":"repository","oa":1,"conference":{"start_date":"2014-01-19","end_date":"2014-01-21","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","location":"San Diego, CA, United States"},"intvolume":" 8318","publication":"VMCAI 2014: Verification, Model Checking, and Abstract Interpretation","volume":8318,"day":"30","arxiv":1,"acknowledgement":" Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publisher":"Springer Nature","publication_identifier":{"isbn":["9783642540127"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783642540134"]},"scopus_import":"1","quality_controlled":"1","title":"Doomsday equilibria for omega-regular games","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Filiot","full_name":"Filiot, Emmanuel","first_name":"Emmanuel"},{"first_name":"Jean-François","full_name":"Raskin, Jean-François","last_name":"Raskin"}],"_id":"10885","page":"78-97","date_created":"2022-03-18T13:03:15Z","article_processing_charge":"No","department":[{"_id":"KrCh"}],"alternative_title":["LNCS"],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-16T10:00:03Z","fulldoi":"https://doi.org/10.1007/978-3-642-54013-4_5","publication_status":"published","month":"01","abstract":[{"text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games.","lang":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"681"}]},"oa_version":"Preprint","type":"conference","external_id":{"arxiv":["1311.3238"]},"date_published":"2014-01-30T00:00:00Z","citation":{"ista":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, 8318:78–97. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_5.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:78-97. doi:10.1007/978-3-642-54013-4_5","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.","short":"K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In VMCAI 2014: Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_5","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:10.1007/978-3-642-54013-4_5."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1311.3238"}],"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"status":"public","doi":"10.1007/978-3-642-54013-4_5","OA_type":"green"},{"day":"19","acknowledgement":"This research is partially supported by the TOPOSYS project FP7-ICT-318493-STREP.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","fulldoi":"https://doi.org/10.1007/978-3-319-04099-8_16","date_updated":"2023-09-05T14:13:16Z","publication":"Topological Methods in Data Analysis and Visualization III ","publication_status":"published","article_processing_charge":"No","alternative_title":["Mathematics and Visualization"],"department":[{"_id":"HeEd"}],"year":"2014","language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-319-04099-8_16","date_published":"2014-03-19T00:00:00Z","date_created":"2022-03-18T13:05:39Z","_id":"10886","page":"249-262","citation":{"mla":"Zobel, Valentin, et al. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–62, doi:10.1007/978-3-319-04099-8_16.","apa":"Zobel, V., Reininghaus, J., & Hotz, I. (2014). Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In Topological Methods in Data Analysis and Visualization III (pp. 249–262). Springer. https://doi.org/10.1007/978-3-319-04099-8_16","ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature,” in Topological Methods in Data Analysis and Visualization III , 2014, pp. 249–262.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, Topological Methods in Data Analysis and Visualization III , Springer, 2014, pp. 249–262.","ista":"Zobel V, Reininghaus J, Hotz I. 2014. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. Topological Methods in Data Analysis and Visualization III . , Mathematics and Visualization, , 249–262.","ama":"Zobel V, Reininghaus J, Hotz I. Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature. In: Topological Methods in Data Analysis and Visualization III . Springer; 2014:249-262. doi:10.1007/978-3-319-04099-8_16","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualization of Two-Dimensional Symmetric Positive Definite Tensor Fields Using the Heat Kernel Signature.” In Topological Methods in Data Analysis and Visualization III , 249–62. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_16."},"quality_controlled":"1","title":"Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature","oa_version":"None","author":[{"first_name":"Valentin","last_name":"Zobel","full_name":"Zobel, Valentin"},{"last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","first_name":"Jan"},{"first_name":"Ingrid","full_name":"Hotz, Ingrid","last_name":"Hotz"}],"type":"conference","month":"03","publisher":"Springer","publication_identifier":{"issn":["1612-3786"],"eisbn":["9783319040998"],"eissn":["2197-666X"],"isbn":["9783319040981"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set."}]},{"date_created":"2022-03-21T07:09:03Z","_id":"10892","page":"117-127","quality_controlled":"1","title":"Planar matchings for weighted straight skeletons","author":[{"first_name":"Therese","full_name":"Biedl, Therese","last_name":"Biedl"},{"orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783319130750"],"issn":["0302-9743"],"isbn":["9783319130743"]},"scopus_import":"1","day":"08","acknowledgement":"T. Biedl was supported by NSERC and the Ross and Muriel Cheriton Fellowship. P. Palfrader was supported by Austrian Science Fund (FWF): P25816-N15.","publication":"25th International Symposium, ISAAC 2014","volume":8889,"conference":{"end_date":"2014-12-17","start_date":"2014-12-15","location":"Jeonju, Korea","name":"ISAAC: International Symposium on Algorithms and Computation"},"intvolume":" 8889","year":"2014","language":[{"iso":"eng"}],"corr_author":"1","status":"public","isi":1,"doi":"10.1007/978-3-319-13075-0_10","date_published":"2014-11-08T00:00:00Z","citation":{"apa":"Biedl, T., Huber, S., & Palfrader, P. (2014). Planar matchings for weighted straight skeletons. In 25th International Symposium, ISAAC 2014 (Vol. 8889, pp. 117–127). Jeonju, Korea: Springer Nature. https://doi.org/10.1007/978-3-319-13075-0_10","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” 25th International Symposium, ISAAC 2014, vol. 8889, Springer Nature, 2014, pp. 117–27, doi:10.1007/978-3-319-13075-0_10.","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” in 25th International Symposium, ISAAC 2014, Jeonju, Korea, 2014, vol. 8889, pp. 117–127.","short":"T. Biedl, S. Huber, P. Palfrader, in:, 25th International Symposium, ISAAC 2014, Springer Nature, 2014, pp. 117–127.","ista":"Biedl T, Huber S, Palfrader P. 2014. Planar matchings for weighted straight skeletons. 25th International Symposium, ISAAC 2014. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 8889, 117–127.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” In 25th International Symposium, ISAAC 2014, 8889:117–27. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13075-0_10.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. In: 25th International Symposium, ISAAC 2014. Vol 8889. Springer Nature; 2014:117-127. doi:10.1007/978-3-319-13075-0_10"},"oa_version":"None","type":"conference","external_id":{"isi":["000354865900010"]},"month":"11","abstract":[{"lang":"eng","text":"In this paper, we introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist.\r\nUsing our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings."}],"related_material":{"record":[{"relation":"later_version","id":"481","status":"public"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1007/978-3-319-13075-0_10","date_updated":"2025-09-29T13:22:55Z","publication_status":"published","article_processing_charge":"No","alternative_title":["LNCS"],"department":[{"_id":"HeEd"}]},{"date_created":"2022-03-21T07:11:23Z","_id":"10893","page":"55-69","scopus_import":"1","publication_identifier":{"eissn":["2197-666X"],"eisbn":["9783319040998"],"issn":["1612-3786"],"isbn":["9783319040981"]},"publisher":"Springer","author":[{"last_name":"Kasten","full_name":"Kasten, Jens","first_name":"Jens"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"full_name":"Reich, Wieland","last_name":"Reich","first_name":"Wieland"},{"full_name":"Scheuermann, Gerik","last_name":"Scheuermann","first_name":"Gerik"}],"title":"Toward the extraction of saddle periodic orbits","quality_controlled":"1","publication":"Topological Methods in Data Analysis and Visualization III ","volume":1,"acknowledgement":"First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program.","day":"19","series_title":"Mathematics and Visualization","place":"Cham","language":[{"iso":"eng"}],"year":"2014","intvolume":" 1","editor":[{"first_name":"Peer-Timo","full_name":"Bremer, Peer-Timo","last_name":"Bremer"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"},{"first_name":"Valerio","full_name":"Pascucci, Valerio","last_name":"Pascucci"},{"last_name":"Peikert","full_name":"Peikert, Ronald","first_name":"Ronald"}],"citation":{"ama":"Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4","ista":"Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69.","chicago":"Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4.","short":"J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69.","ieee":"J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.","mla":"Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4.","apa":"Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4"},"date_published":"2014-03-19T00:00:00Z","doi":"10.1007/978-3-319-04099-8_4","project":[{"name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","abstract":[{"lang":"eng","text":"Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data."}],"month":"03","type":"book_chapter","oa_version":"None","publication_status":"published","fulldoi":"https://doi.org/10.1007/978-3-319-04099-8_4","date_updated":"2025-04-15T08:37:54Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"article_processing_charge":"No"},{"intvolume":" 8592","conference":{"name":"ICMS: International Congress on Mathematical Software","location":"Seoul, South Korea","end_date":"2014-08-09","start_date":"2014-08-05"},"place":"Berlin, Heidelberg","language":[{"iso":"eng"}],"year":"2014","day":"01","series_title":"LNCS","volume":8592,"publication":"ICMS 2014: International Congress on Mathematical Software","author":[{"orcid":"0000-0002-9683-0724","first_name":"Ulrich","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan","last_name":"Reininghaus"},{"first_name":"Hubert","full_name":"Wagner, Hubert","last_name":"Wagner"}],"title":"PHAT – Persistent Homology Algorithms Toolbox","quality_controlled":"1","scopus_import":"1","publication_identifier":{"isbn":["9783662441985"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783662441992"]},"publisher":"Springer Berlin Heidelberg","date_created":"2022-03-21T07:12:16Z","_id":"10894","page":"137-143","department":[{"_id":"HeEd"}],"article_processing_charge":"No","publication_status":"published","fulldoi":"https://doi.org/10.1007/978-3-662-44199-2_24","date_updated":"2026-06-18T17:35:15Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","oa_version":"None","related_material":{"record":[{"status":"public","id":"1433","relation":"later_version"}]},"abstract":[{"lang":"eng","text":"PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations."}],"month":"09","doi":"10.1007/978-3-662-44199-2_24","status":"public","citation":{"apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2014). PHAT – Persistent Homology Algorithms Toolbox. In ICMS 2014: International Congress on Mathematical Software (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-44199-2_24","mla":"Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” ICMS 2014: International Congress on Mathematical Software, vol. 8592, Springer Berlin Heidelberg, 2014, pp. 137–43, doi:10.1007/978-3-662-44199-2_24.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms Toolbox. In: ICMS 2014: International Congress on Mathematical Software. Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143. doi:10.1007/978-3-662-44199-2_24","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software. ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT – Persistent Homology Algorithms Toolbox.” In ICMS 2014: International Congress on Mathematical Software, 8592:137–43. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. https://doi.org/10.1007/978-3-662-44199-2_24.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 137–143.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology Algorithms Toolbox,” in ICMS 2014: International Congress on Mathematical Software, Seoul, South Korea, 2014, vol. 8592, pp. 137–143."},"date_published":"2014-09-01T00:00:00Z"},{"month":"04","related_material":{"record":[{"status":"public","id":"5405","relation":"earlier_version"}]},"abstract":[{"lang":"eng","text":"The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2 1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic). We present an algorithm running in time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which the objective can be ensured with probability 1, where n is the number of states of the game, d the number of priorities of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states in 2 1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective). "}],"publist_id":"4758","oa_version":"None","type":"conference","date_published":"2014-04-01T00:00:00Z","citation":{"ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 210–225.","short":"K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp. 210–225.","ama":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:10.1007/978-3-642-54830-7_14","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. “Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_14.","ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 210–225.","mla":"Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff Parity Games. Vol. 8412, Springer, 2014, pp. 210–25, doi:10.1007/978-3-642-54830-7_14.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2014). Perfect-information stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_14"},"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"status":"public","doi":"10.1007/978-3-642-54830-7_14","department":[{"_id":"KrCh"}],"alternative_title":["LNCS"],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:24:50Z","fulldoi":"https://doi.org/10.1007/978-3-642-54830-7_14","publication_status":"published","publisher":"Springer","scopus_import":1,"quality_controlled":"1","title":"Perfect-information stochastic mean-payoff parity games","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"first_name":"Hugo","full_name":"Gimbert, Hugo","last_name":"Gimbert"},{"first_name":"Youssouf","full_name":"Oualhadj, Youssouf","last_name":"Oualhadj"}],"date_created":"2018-12-11T11:56:21Z","_id":"2212","page":"210 - 225","year":"2014","language":[{"iso":"eng"}],"conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures","location":"Grenoble, France","end_date":"2014-04-13","start_date":"2014-04-05"},"intvolume":" 8412","volume":8412,"day":"01","acknowledgement":"This research was supported by European project Cassting (FP7-601148).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128."},{"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","fulldoi":"https://doi.org/10.1007/978-3-642-54830-7_16","date_updated":"2023-02-23T12:24:58Z","alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"status":"public","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.3289"}],"doi":"10.1007/978-3-642-54830-7_16","date_published":"2014-04-01T00:00:00Z","citation":{"short":"K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257.","ieee":"K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation stochastic parity games with finite-memory strategies,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 242–257.","ama":"Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation stochastic parity games with finite-memory strategies. In: Vol 8412. Springer; 2014:242-257. doi:10.1007/978-3-642-54830-7_16","ista":"Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 242–257.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,” 8412:242–57. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_16.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies. Vol. 8412, Springer, 2014, pp. 242–57, doi:10.1007/978-3-642-54830-7_16.","apa":"Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2014). The complexity of partial-observation stochastic parity games with finite-memory strategies (Vol. 8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_16"},"oa_version":"Preprint","publist_id":"4757","type":"conference","external_id":{"arxiv":["1401.3289"]},"month":"04","related_material":{"record":[{"relation":"earlier_version","id":"5408","status":"public"}]},"abstract":[{"lang":"eng","text":"We consider two-player partial-observation stochastic games on finitestate graphs where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are ε-regular conditions specified as parity objectives. The qualitative-analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). These qualitative-analysis problems are known to be undecidable. However in many applications the relevant question is the existence of finite-memory strategies, and the qualitative-analysis problems under finite-memory strategies was recently shown to be decidable in 2EXPTIME.We improve the complexity and show that the qualitative-analysis problems for partial-observation stochastic parity games under finite-memory strategies are EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis."}],"acknowledgement":"This research was supported by European project Cassting (FP7-601148), NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","day":"01","arxiv":1,"volume":8412,"conference":{"location":"Grenoble, France","name":"FoSSaCS: Foundations of Software Science and Computation Structures","end_date":"2014-04-13","start_date":"2014-04-05"},"oa":1,"intvolume":" 8412","year":"2014","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:21Z","_id":"2213","page":"242 - 257","title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","quality_controlled":"1","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"first_name":"Sumit","last_name":"Nain","full_name":"Nain, Sumit"},{"first_name":"Moshe","last_name":"Vardi","full_name":"Vardi, Moshe"}],"publisher":"Springer","scopus_import":1}]