[{"publication":"Heredity","date_updated":"2025-04-15T07:11:02Z","publisher":"Nature Publishing Group","year":"2017","title":"How does epistasis influence the response to selection?","citation":{"short":"N.H. Barton, Heredity 118 (2017) 96–109.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” <i>Heredity</i>, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>.","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>.","ama":"Barton NH. How does epistasis influence the response to selection? <i>Heredity</i>. 2017;118:96-109. doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>","ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109."},"external_id":{"isi":["000392229100011"]},"publist_id":"6151","author":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"doi":"10.1038/hdy.2016.109","month":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","ec_funded":1,"_id":"1199","day":"01","date_created":"2018-12-11T11:50:40Z","oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_published":"2017-01-01T00:00:00Z","isi":1,"department":[{"_id":"NiBa"}],"scopus_import":"1","type":"journal_article","status":"public","intvolume":"       118","related_material":{"record":[{"status":"public","id":"9710","relation":"research_data"}]},"volume":118,"quality_controlled":"1","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/"}],"page":"96 - 109","language":[{"iso":"eng"}],"oa_version":"Submitted Version","abstract":[{"text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.","lang":"eng"}]},{"oa":1,"pubrep_id":"722","date_created":"2018-12-11T11:50:43Z","ddc":["530"],"day":"01","_id":"1207","ec_funded":1,"publication_status":"published","file":[{"checksum":"ddff79154c3daf27237de5383b1264a9","creator":"system","content_type":"application/pdf","file_size":1033743,"relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:14:47Z","date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2016-722-v1+1_s00220-016-2805-6.pdf","file_id":"5102"}],"issue":"3","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475","first_name":"Zhigang"},{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös"},{"first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","last_name":"Schnelli"}],"publist_id":"6141","doi":"10.1007/s00220-016-2805-6","citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition of Random Matrices on Optimal Scale.” <i>Communications in Mathematical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00220-016-2805-6\">https://doi.org/10.1007/s00220-016-2805-6</a>.","ama":"Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal scale. <i>Communications in Mathematical Physics</i>. 2017;349(3):947-990. doi:<a href=\"https://doi.org/10.1007/s00220-016-2805-6\">10.1007/s00220-016-2805-6</a>","ista":"Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2017). Local law of addition of random matrices on optimal scale. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2805-6\">https://doi.org/10.1007/s00220-016-2805-6</a>","short":"Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349 (2017) 947–990.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices on optimal scale,” <i>Communications in Mathematical Physics</i>, vol. 349, no. 3. Springer, pp. 947–990, 2017.","mla":"Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.” <i>Communications in Mathematical Physics</i>, vol. 349, no. 3, Springer, 2017, pp. 947–90, doi:<a href=\"https://doi.org/10.1007/s00220-016-2805-6\">10.1007/s00220-016-2805-6</a>."},"external_id":{"isi":["000393696700005"]},"title":"Local law of addition of random matrices on optimal scale","publication_identifier":{"issn":["0010-3616"]},"year":"2017","date_updated":"2025-07-10T11:50:22Z","publisher":"Springer","publication":"Communications in Mathematical Physics","abstract":[{"lang":"eng","text":"The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix."}],"file_date_updated":"2020-07-14T12:44:39Z","oa_version":"Published Version","language":[{"iso":"eng"}],"page":"947 - 990","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":349,"intvolume":"       349","type":"journal_article","status":"public","scopus_import":"1","isi":1,"department":[{"_id":"LaEr"}],"date_published":"2017-02-01T00:00:00Z","has_accepted_license":"1","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}]},{"quality_controlled":"1","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1408.5604","open_access":"1"}],"language":[{"iso":"eng"}],"page":"1269 - 1292","oa_version":"Submitted Version","abstract":[{"text":"We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ&gt;1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd.","lang":"eng"}],"status":"public","type":"journal_article","volume":79,"intvolume":"        79","date_published":"2017-09-01T00:00:00Z","arxiv":1,"department":[{"_id":"CaUh"}],"isi":1,"scopus_import":"1","project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications","grant_number":"Y 903-N35"}],"_id":"1208","day":"01","date_created":"2018-12-11T11:50:43Z","oa":1,"issue":"4","publication_status":"published","citation":{"mla":"Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>.","ieee":"P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017.","apa":"Zwiernik, P., Uhler, C., &#38; Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>","short":"P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.","ista":"Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.","ama":"Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society Series B: Statistical Methodology</i>. 2017;79(4):1269-1292. doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>","chicago":"Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>."},"external_id":{"isi":["000411712300012"],"arxiv":["1408.5604"]},"doi":"10.1111/rssb.12217","author":[{"first_name":"Piotr","last_name":"Zwiernik","full_name":"Zwiernik, Piotr"},{"first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline"},{"first_name":"Donald","last_name":"Richards","full_name":"Richards, Donald"}],"publist_id":"6142","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of the Royal Statistical Society. Series B: Statistical Methodology","publisher":"Wiley-Blackwell","date_updated":"2025-06-04T09:41:22Z","year":"2017","corr_author":"1","publication_identifier":{"issn":["1369-7412"]},"title":"Maximum likelihood estimation for linear Gaussian covariance models"},{"month":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"6136","author":[{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cvitanović, Predrag","last_name":"Cvitanović","first_name":"Predrag"}],"doi":"10.1007/s10955-016-1672-z","citation":{"ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. 2017;167(3-4):636-655. doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>.","apa":"Budanur, N. B., &#38; Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655."},"external_id":{"isi":["000400233600014"]},"title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","year":"2017","date_updated":"2025-09-22T09:36:50Z","publisher":"Springer","publication":"Journal of Statistical Physics","oa":1,"pubrep_id":"782","date_created":"2018-12-11T11:50:44Z","ddc":["530"],"day":"01","_id":"1211","publication_status":"published","file":[{"relation":"main_file","file_size":2820207,"date_created":"2018-12-12T10:18:01Z","access_level":"open_access","checksum":"3e971d09eb167761aa0888ed415b0056","content_type":"application/pdf","creator":"system","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","file_id":"5319","date_updated":"2020-07-14T12:44:39Z"}],"issue":"3-4","scopus_import":"1","department":[{"_id":"BjHo"}],"isi":1,"acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","date_published":"2017-05-01T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:39Z","abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"page":"636-655","article_processing_charge":"No","quality_controlled":"1","intvolume":"       167","volume":167,"type":"journal_article","status":"public"},{"publication_identifier":{"issn":["0091-679X"]},"acknowledged_ssus":[{"_id":"Bio"}],"title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","editor":[{"full_name":"Echard, Arnaud ","last_name":"Echard","first_name":"Arnaud "}],"publication":"Cytokinesis","date_updated":"2025-07-10T11:50:24Z","publisher":"Academic Press","year":"2017","doi":"10.1016/bs.mcb.2016.03.036","publist_id":"6134","author":[{"first_name":"Natalia","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia","last_name":"Baranova"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” <i>Cytokinesis</i>, edited by Arnaud  Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>.","ieee":"N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in <i>Cytokinesis</i>, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370.","apa":"Baranova, N. S., &#38; Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), <i>Cytokinesis</i> (Vol. 137, pp. 355–370). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>","short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370.","ista":"Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370.","ama":"Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. <i>Cytokinesis</i>. Vol 137. Academic Press; 2017:355-370. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>","chicago":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In <i>Cytokinesis</i>, edited by Arnaud  Echard, 137:355–70. Academic Press, 2017. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>."},"external_id":{"isi":["000403542900022"]},"publication_status":"published","date_created":"2018-12-11T11:50:45Z","ec_funded":1,"_id":"1213","day":"01","project":[{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"department":[{"_id":"MaLo"}],"isi":1,"scopus_import":"1","date_published":"2017-12-01T00:00:00Z","acknowledgement":"Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).","volume":137,"intvolume":"       137","alternative_title":["Methods in Cell Biology"],"status":"public","type":"book_chapter","page":"355 - 370","language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin."}],"quality_controlled":"1","article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","author":[{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"}],"publist_id":"7628","citation":{"ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory  vol. 75, 228–249.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: <i>Proceedings of the 31st Conference On Learning Theory</i>. Vol 75. ML Research Press; 2017:228-249.","chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In <i>Proceedings of the 31st Conference On Learning Theory</i>, 75:228–49. ML Research Press, 2017.","mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” <i>Proceedings of the 31st Conference On Learning Theory</i>, vol. 75, ML Research Press, 2017, pp. 228–49.","ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in <i>Proceedings of the 31st Conference On Learning Theory</i>, 2017, vol. 75, pp. 228–249.","apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In <i>Proceedings of the 31st Conference On Learning Theory</i> (Vol. 75, pp. 228–249). ML Research Press.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249."},"external_id":{"arxiv":["1608.04223"]},"title":"A faster approximation algorithm for the Gibbs partition function","year":"2017","publisher":"ML Research Press","date_updated":"2024-11-04T13:52:32Z","publication":"Proceedings of the 31st Conference On Learning Theory","oa":1,"date_created":"2018-12-11T11:45:33Z","ddc":["510"],"day":"27","_id":"274","ec_funded":1,"conference":{"end_date":"2018-07-09","start_date":"2018-07-06","name":"COLT: Annual Conference on Learning Theory "},"publication_status":"published","file":[{"relation":"main_file","file_size":408974,"date_created":"2020-05-12T09:23:27Z","access_level":"open_access","checksum":"89db06a0e8083524449cb59b56bf4e5b","creator":"dernst","content_type":"application/pdf","file_name":"2018_PMLR_Kolmogorov.pdf","file_id":"7820","date_updated":"2020-07-14T12:45:45Z"}],"department":[{"_id":"VlKo"}],"arxiv":1,"date_published":"2017-12-27T00:00:00Z","has_accepted_license":"1","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"file_date_updated":"2020-07-14T12:45:45Z","abstract":[{"text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation.","lang":"eng"}],"oa_version":"Published Version","page":"228-249","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":75,"intvolume":"        75","status":"public","type":"conference"},{"alternative_title":["Journal of Physics: Conference Series"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":999,"intvolume":"       999","related_material":{"record":[{"status":"public","id":"6013","relation":"later_version"}]},"type":"conference","status":"public","abstract":[{"text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","quality_controlled":"1","scopus_import":"1","isi":1,"department":[{"_id":"MiLe"}],"article_number":"012004","date_published":"2017-07-14T00:00:00Z","arxiv":1,"has_accepted_license":"1","publication_status":"published","issue":"1","file":[{"file_size":949321,"relation":"main_file","date_created":"2019-01-22T08:34:10Z","access_level":"open_access","content_type":"application/pdf","checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","creator":"dernst","file_id":"5871","file_name":"2017_Physics_Camus.pdf","date_updated":"2020-07-14T12:46:00Z"}],"oa":1,"ddc":["530"],"date_created":"2018-12-11T11:45:46Z","_id":"313","day":"14","conference":{"start_date":"2017-08-17","end_date":"2017-08-21","location":"Kazan, Russian Federation","name":"Annual International Laser Physics Workshop LPHYS"},"publication_identifier":{"issn":["1742-6588"]},"title":"Experimental evidence for Wigner's tunneling time","date_updated":"2025-09-18T10:29:07Z","publisher":"American Physical Society","year":"2017","author":[{"first_name":"Nicolas","last_name":"Camus","full_name":"Camus, Nicolas"},{"last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","orcid":"0000-0001-5973-0874"},{"full_name":"Fechner, Lutz","last_name":"Fechner","first_name":"Lutz"},{"full_name":"Klaiber, Michael","last_name":"Klaiber","first_name":"Michael"},{"last_name":"Laux","full_name":"Laux, Martin","first_name":"Martin"},{"first_name":"Yonghao","last_name":"Mi","full_name":"Mi, Yonghao"},{"first_name":"Karen","last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen"},{"full_name":"Pfeifer, Thomas","last_name":"Pfeifer","first_name":"Thomas"},{"first_name":"Cristoph","last_name":"Keitel","full_name":"Keitel, Cristoph"},{"full_name":"Moshammer, Robert","last_name":"Moshammer","first_name":"Robert"}],"doi":"10.1088/1742-6596/999/1/012004","publist_id":"7552","month":"07","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>.","mla":"Camus, Nicolas, et al. <i>Experimental Evidence for Wigner’s Tunneling Time</i>. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>.","ieee":"N. Camus <i>et al.</i>, “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017."},"external_id":{"arxiv":["1611.03701"],"isi":["000432427200004"]}},{"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"pmid":1,"scopus_import":"1","isi":1,"department":[{"_id":"ToHe"}],"date_published":"2017-06-01T00:00:00Z","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":50,"intvolume":"        50","related_material":{"record":[{"relation":"earlier_version","id":"1729","status":"public"}]},"status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively."}],"file_date_updated":"2020-07-14T12:44:44Z","oa_version":"Published Version","page":"97 - 139","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","title":"From non-preemptive to preemptive scheduling using synchronization synthesis","year":"2017","corr_author":"1","publisher":"Springer","date_updated":"2025-09-23T08:54:01Z","publication":"Formal Methods in System Design","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s10703-016-0256-5","publist_id":"5929","author":[{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Edmund","last_name":"Clarke","full_name":"Clarke, Edmund"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","first_name":"Arjun"},{"first_name":"Leonid","full_name":"Ryzhyk, Leonid","last_name":"Ryzhyk"},{"first_name":"Roopsha","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta"},{"last_name":"Tarrach","full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","orcid":"0000-0003-4409-8487"}],"external_id":{"pmid":["28490835"],"isi":["000399888900001"]},"citation":{"ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. 2017;50(2-3):97-139. doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139."},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:44:44Z","file_id":"4985","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","relation":"main_file","file_size":1416170,"access_level":"open_access","date_created":"2018-12-12T10:13:05Z","creator":"system","checksum":"1163dfd997e8212c789525d4178b1653","content_type":"application/pdf"}],"issue":"2-3","pubrep_id":"656","oa":1,"date_created":"2018-12-11T11:51:27Z","ddc":["000"],"day":"01","_id":"1338","ec_funded":1},{"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"isi":1,"scopus_import":"1","has_accepted_license":"1","date_published":"2017-12-01T00:00:00Z","volume":54,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"        54","related_material":{"record":[{"status":"public","id":"1835","relation":"earlier_version"}]},"status":"public","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"page":"765 - 787","file_date_updated":"2020-07-14T12:44:46Z","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"quality_controlled":"1","article_processing_charge":"No","title":"Model checking the evolution of gene regulatory networks","publication_identifier":{"issn":["0001-5903"]},"publication":"Acta Informatica","corr_author":"1","year":"2017","date_updated":"2025-07-10T11:50:42Z","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","author":[{"last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","first_name":"Mirco","orcid":"0000-0001-8180-0904"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"},{"first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago"},{"last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","first_name":"Tatjana"}],"doi":"10.1007/s00236-016-0278-x","publist_id":"5898","citation":{"short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” <i>Acta Informatica</i>, vol. 54, no. 8. Springer, pp. 765–787, 2017.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787. doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787."},"external_id":{"isi":["000414343200003"]},"file":[{"checksum":"4e661d9135d7f8c342e8e258dee76f3e","creator":"dernst","content_type":"application/pdf","file_size":755241,"relation":"main_file","date_created":"2019-01-17T15:57:29Z","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","file_id":"5841","file_name":"2017_ActaInformatica_Giacobbe.pdf"}],"issue":"8","publication_status":"published","date_created":"2018-12-11T11:51:32Z","ddc":["006","576"],"pubrep_id":"649","oa":1,"ec_funded":1,"day":"01","_id":"1351"},{"publist_id":"5873","doi":"10.1111/cgf.12941","author":[{"first_name":"Pierre","last_name":"Manteaux","full_name":"Manteaux, Pierre"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"last_name":"Narain","full_name":"Narain, Rahul","first_name":"Rahul"},{"first_name":"Stéphane","last_name":"Redon","full_name":"Redon, Stéphane"},{"last_name":"Faure","full_name":"Faure, François","first_name":"François"},{"first_name":"Marie","last_name":"Cani","full_name":"Cani, Marie"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"09","external_id":{"isi":["000408634200019"]},"citation":{"mla":"Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” <i>Computer Graphics Forum</i>, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:<a href=\"https://doi.org/10.1111/cgf.12941\">10.1111/cgf.12941</a>.","ieee":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” <i>Computer Graphics Forum</i>, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","apa":"Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., &#38; Cani, M. (2017). Adaptive physically based models in computer graphics. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/cgf.12941\">https://doi.org/10.1111/cgf.12941</a>","ista":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.","ama":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. <i>Computer Graphics Forum</i>. 2017;36(6):312-337. doi:<a href=\"https://doi.org/10.1111/cgf.12941\">10.1111/cgf.12941</a>","chicago":"Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/cgf.12941\">https://doi.org/10.1111/cgf.12941</a>."},"publication_identifier":{"issn":["01677055"]},"title":"Adaptive physically based models in computer graphics","publication":"Computer Graphics Forum","date_updated":"2023-09-20T11:05:36Z","publisher":"Wiley-Blackwell","year":"2017","ddc":["000"],"date_created":"2018-12-11T11:51:37Z","oa":1,"pubrep_id":"634","_id":"1367","day":"01","issue":"6","file":[{"relation":"main_file","file_size":1434439,"date_created":"2018-12-12T10:16:21Z","access_level":"open_access","content_type":"application/pdf","checksum":"7676e9a9ead6d58c3000988c97deb2ef","creator":"system","date_updated":"2020-07-14T12:44:47Z","file_id":"5208","file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf"}],"publication_status":"published","department":[{"_id":"ChWo"}],"isi":1,"scopus_import":"1","has_accepted_license":"1","date_published":"2017-09-01T00:00:00Z","acknowledgement":"This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209).","page":"312 - 337","language":[{"iso":"eng"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids."}],"file_date_updated":"2020-07-14T12:44:47Z","quality_controlled":"1","article_processing_charge":"No","intvolume":"        36","volume":36,"status":"public","type":"journal_article"},{"external_id":{"isi":["000390637000014"],"arxiv":["1410.5387"]},"citation":{"ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>.","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &#38; Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23(2):230-253. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>"},"doi":"10.1016/j.nahs.2016.04.006","author":[{"first_name":"Mária","last_name":"Svoreňová","full_name":"Svoreňová, Mária"},{"last_name":"Kretinsky","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Cěrná","full_name":"Cěrná, Ivana","first_name":"Ivana"},{"full_name":"Belta, Cǎlin","last_name":"Belta","first_name":"Cǎlin"}],"publist_id":"5800","month":"02","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","date_updated":"2025-06-11T06:33:00Z","year":"2017","publication":"Nonlinear Analysis: Hybrid Systems","title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","_id":"1407","day":"01","ec_funded":1,"oa":1,"date_created":"2018-12-11T11:51:50Z","publication_status":"published","issue":"2","arxiv":1,"date_published":"2017-02-01T00:00:00Z","scopus_import":"1","isi":1,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study."}],"language":[{"iso":"eng"}],"page":"230 - 253","main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"oa_version":"Preprint","status":"public","type":"journal_article","volume":23,"intvolume":"        23","related_material":{"record":[{"relation":"earlier_version","id":"1689","status":"public"}]}},{"publication_status":"published","oa":1,"date_created":"2018-12-11T11:51:59Z","day":"01","_id":"1433","ec_funded":1,"OA_type":"free access","title":"Phat - Persistent homology algorithms toolbox","publication_identifier":{"issn":[" 0747-7171"]},"corr_author":"1","year":"2017","date_updated":"2025-10-01T07:39:51Z","publisher":"Academic Press","publication":"Journal of Symbolic Computation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","doi":"10.1016/j.jsc.2016.03.008","author":[{"full_name":"Bauer, Ulrich","last_name":"Bauer","first_name":"Ulrich"},{"first_name":"Michael","full_name":"Kerber, Michael","last_name":"Kerber"},{"first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","last_name":"Wagner"}],"publist_id":"5765","external_id":{"isi":["000384396000005"]},"citation":{"mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>, vol. 78, Academic Press, 2017, pp. 76–90, doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” <i>Journal of Symbolic Computation</i>, vol. 78. Academic Press, pp. 76–90, 2017.","apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. 2017;78:76-90. doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>."},"intvolume":"        78","volume":78,"related_material":{"record":[{"id":"10894","relation":"earlier_version","status":"public"}]},"type":"journal_article","status":"public","abstract":[{"text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology.","lang":"eng"}],"oa_version":"Published Version","page":"76 - 90","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jsc.2016.03.008"}],"article_processing_charge":"No","article_type":"original","quality_controlled":"1","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"scopus_import":"1","department":[{"_id":"HeEd"}],"isi":1,"acknowledgement":"Michael Kerber acknowledges support by the Max Planck Center for Visual Computing and Communications (FKZ-01IMC01 and FKZ-01IM10001). Ulrich Bauer, Jan Reininghaus, and Hubert Wagner acknowledge support by the EU Project TOPOSYS (FP7-ICT-318493-STREP).","date_published":"2017-01-01T00:00:00Z"},{"article_processing_charge":"No","article_type":"review","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:39Z","abstract":[{"text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.","lang":"eng"}],"oa_version":"Published Version","page":"45 - 57","language":[{"iso":"eng"}],"status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":45,"intvolume":"        45","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","date_published":"2017-01-01T00:00:00Z","has_accepted_license":"1","scopus_import":"1","isi":1,"department":[{"_id":"GaNo"}],"pmid":1,"day":"01","_id":"1228","pubrep_id":"738","oa":1,"date_created":"2018-12-11T11:50:50Z","ddc":["616"],"publication_status":"published","file":[{"file_id":"4838","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","date_updated":"2020-07-14T12:44:39Z","relation":"main_file","file_size":169145,"date_created":"2018-12-12T10:10:48Z","access_level":"open_access","checksum":"c572cf02be8fbb7020cfcfb892182e4c","creator":"system","content_type":"application/pdf"}],"issue":"1","external_id":{"pmid":["27690184"],"isi":["000392487100005"]},"citation":{"apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>.","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"01","publist_id":"6106","doi":"10.1111/ejn.13418","author":[{"full_name":"Sauerzopf, Ulrich","last_name":"Sauerzopf","first_name":"Ulrich"},{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","last_name":"Sacco","first_name":"Roberto"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia"},{"full_name":"Niello, Marco","last_name":"Niello","first_name":"Marco"},{"last_name":"Weidenauer","full_name":"Weidenauer, Ana","first_name":"Ana"},{"full_name":"Praschak Rieder, Nicole","last_name":"Praschak Rieder","first_name":"Nicole"},{"full_name":"Sitte, Harald","last_name":"Sitte","first_name":"Harald"},{"first_name":"Matthaeus","full_name":"Willeit, Matthaeus","last_name":"Willeit"}],"year":"2017","publisher":"Wiley-Blackwell","date_updated":"2023-09-20T11:16:01Z","publication":"European Journal of Neuroscience","title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence"},{"type":"conference_abstract","status":"public","file":[{"file_id":"12969","file_name":"2017_AHPC_Schloegl.pdf","success":1,"date_updated":"2023-05-16T07:20:50Z","creator":"dernst","content_type":"application/pdf","checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","access_level":"open_access","date_created":"2023-05-16T07:20:50Z","file_size":1005486,"relation":"main_file"}],"publication_status":"published","conference":{"location":"Grundlsee, Austria","name":"AHPC: Austrian HPC Meeting","start_date":"2017-03-01","end_date":"2017-03-03"},"article_processing_charge":"No","_id":"12905","day":"03","page":"28","language":[{"iso":"eng"}],"ddc":["000"],"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf"}],"oa_version":"Published Version","date_created":"2023-05-05T12:58:53Z","oa":1,"file_date_updated":"2023-05-16T07:20:50Z","publication":"AHPC17 – Austrian HPC Meeting 2017","publisher":"FSP Scientific Computing","date_updated":"2024-10-09T21:05:23Z","corr_author":"1","year":"2017","title":"Scientific Computing at IST Austria","has_accepted_license":"1","date_published":"2017-03-03T00:00:00Z","citation":{"apa":"Schlögl, A., &#38; Kiss, J. (2017). Scientific Computing at IST Austria. In <i>AHPC17 – Austrian HPC Meeting 2017</i> (p. 28). Grundlsee, Austria: FSP Scientific Computing.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in <i>AHPC17 – Austrian HPC Meeting 2017</i>, Grundlsee, Austria, 2017, p. 28.","mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” <i>AHPC17 – Austrian HPC Meeting 2017</i>, FSP Scientific Computing, 2017, p. 28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In <i>AHPC17 – Austrian HPC Meeting 2017</i>, 28. FSP Scientific Computing, 2017.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: <i>AHPC17 – Austrian HPC Meeting 2017</i>. FSP Scientific Computing; 2017:28.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28."},"department":[{"_id":"ScienComp"}],"author":[{"first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"first_name":"Janos","full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss"}],"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","file":[{"access_level":"open_access","date_created":"2018-12-12T10:11:30Z","file_size":708657,"relation":"main_file","content_type":"application/pdf","checksum":"91271b23cf884d7c06d33bef0cd623b1","creator":"system","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","file_id":"4885","date_updated":"2020-07-14T12:44:42Z"}],"pubrep_id":"717","oa":1,"date_created":"2018-12-11T11:51:12Z","ddc":["004","006"],"day":"01","_id":"1294","ec_funded":1,"title":"Trading performance for stability in Markov decision processes","year":"2017","date_updated":"2025-09-29T14:16:56Z","publisher":"Elsevier","publication":"Journal of Computer and System Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"03","author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"}],"doi":"10.1016/j.jcss.2016.09.009","publist_id":"6009","external_id":{"isi":["000388430000011"]},"citation":{"apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170."},"volume":84,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"related_material":{"record":[{"status":"public","id":"2305","relation":"earlier_version"}]},"intvolume":"        84","type":"journal_article","status":"public","abstract":[{"text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:42Z","oa_version":"Published Version","language":[{"iso":"eng"}],"page":"144 - 170","article_processing_charge":"No","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","isi":1,"department":[{"_id":"KrCh"}],"date_published":"2017-03-01T00:00:00Z","has_accepted_license":"1"},{"abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"oa_version":"Preprint","page":"443-460","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"article_processing_charge":"No","quality_controlled":"1","alternative_title":["LNCS"],"volume":10205,"intvolume":"     10205","type":"conference","status":"public","department":[{"_id":"KrCh"}],"isi":1,"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","date_published":"2017-03-31T00:00:00Z","arxiv":1,"oa":1,"date_created":"2023-06-21T13:21:14Z","day":"31","_id":"13160","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Uppsala, Sweden","start_date":"2017-04-22","end_date":"2017-04-29"},"publication_status":"published","month":"03","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/978-3-662-54577-5_26","author":[{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan"},{"orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"first_name":"Clara","last_name":"Waldmann","full_name":"Waldmann, Clara"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"}],"external_id":{"isi":["000440734900026"],"arxiv":["1701.05738"]},"citation":{"ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460."},"title":"Index appearance record for transforming Rabin automata into parity automata","publication_identifier":{"eisbn":["9783662545775"],"eissn":["1611-3349"],"isbn":["9783662545768"],"issn":["0302-9743"]},"corr_author":"1","year":"2017","date_updated":"2025-09-18T10:42:48Z","publisher":"Springer","publication":"Tools and Algorithms for the Construction and Analysis of Systems"},{"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Uecker","full_name":"Uecker, Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard"}],"publist_id":"6327","doi":"10.1111/evo.13191","external_id":{"isi":["000398545200003"]},"citation":{"ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>.","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. 2017;71(4):845-858. doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” <i>Evolution</i>, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>.","short":"H. Uecker, Evolution 71 (2017) 845–858.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>"},"title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","publication_identifier":{"issn":["0014-3820"]},"publication":"Evolution","year":"2017","publisher":"Wiley-Blackwell","date_updated":"2025-07-10T11:49:52Z","date_created":"2018-12-11T11:49:57Z","oa":1,"ec_funded":1,"day":"01","_id":"1063","issue":"4","publication_status":"published","isi":1,"department":[{"_id":"NiBa"}],"scopus_import":"1","date_published":"2017-04-01T00:00:00Z","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"language":[{"iso":"eng"}],"page":"845 - 858","abstract":[{"lang":"eng","text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations."}],"quality_controlled":"1","article_processing_charge":"No","volume":71,"intvolume":"        71","type":"journal_article","status":"public"},{"department":[{"_id":"KrCh"},{"_id":"HeEd"}],"isi":1,"scopus_import":"1","has_accepted_license":"1","date_published":"2017-06-01T00:00:00Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"page":"25 - 29","oa_version":"Submitted Version","file_date_updated":"2019-10-15T07:44:51Z","abstract":[{"lang":"eng","text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs."}],"quality_controlled":"1","article_processing_charge":"No","volume":122,"intvolume":"       122","type":"journal_article","status":"public","publist_id":"6323","doi":"10.1016/j.ipl.2017.02.003","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8882-5116","first_name":"Georg F","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang"}],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. <i>Information Processing Letters</i>. 2017;122:25-29. doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">https://doi.org/10.1016/j.ipl.2017.02.003</a>.","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>, vol. 122, Elsevier, 2017, pp. 25–29, doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>.","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” <i>Information Processing Letters</i>, vol. 122. Elsevier, pp. 25–29, 2017.","apa":"Chatterjee, K., &#38; Osang, G. F. (2017). Pushdown reachability with constant treewidth. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">https://doi.org/10.1016/j.ipl.2017.02.003</a>","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29."},"external_id":{"isi":["000399506600005"]},"publication_identifier":{"issn":["0020-0190"]},"title":"Pushdown reachability with constant treewidth","publication":"Information Processing Letters","publisher":"Elsevier","date_updated":"2025-07-10T11:49:53Z","year":"2017","ddc":["000"],"date_created":"2018-12-11T11:49:57Z","pubrep_id":"991","oa":1,"ec_funded":1,"_id":"1065","day":"01","file":[{"date_updated":"2019-10-15T07:44:51Z","file_id":"4998","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","access_level":"open_access","date_created":"2018-12-12T10:13:17Z","relation":"main_file","file_size":247657,"content_type":"application/pdf","creator":"system"}],"publication_status":"published"},{"day":"01","_id":"1066","OA_type":"free access","ec_funded":1,"oa":1,"date_created":"2018-12-11T11:49:58Z","publication_status":"published","issue":"2","external_id":{"isi":["000402025600002"]},"citation":{"ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. <i>Information and Computation</i>. 2017;254(2):143-166. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2017). Quantitative fair simulation games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” <i>Information and Computation</i>, vol. 254, no. 2. Elsevier, pp. 143–166, 2017."},"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.ic.2016.10.006","publist_id":"6322","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"corr_author":"1","year":"2017","date_updated":"2025-06-25T11:18:09Z","publisher":"Elsevier","publication":"Information and Computation","title":"Quantitative fair simulation games","article_processing_charge":"No","article_type":"original","quality_controlled":"1","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ic.2016.10.006"}],"page":"143 - 166","status":"public","type":"journal_article","volume":254,"intvolume":"       254","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5428"}]},"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreements 267989 (QUAREM), 279307 (Graph Games), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), S11407-N23 (RiSE), P23499-N23, and Microsoft faculty fellows award.","date_published":"2017-06-01T00:00:00Z","scopus_import":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"isi":1,"OA_place":"publisher","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}]},{"publisher":"Cell Press","date_updated":"2025-07-10T11:49:55Z","year":"2017","corr_author":"1","publication":"Developmental Cell","publication_identifier":{"issn":["1534-5807"]},"acknowledged_ssus":[{"_id":"PreCl"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","citation":{"ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. 2017;40(4):354-366. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” <i>Developmental Cell</i>, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>.","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., &#38; Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366."},"external_id":{"isi":["000395368300007"]},"author":[{"last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","first_name":"Hitoshi"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"first_name":"Martin","last_name":"Bock","full_name":"Bock, Martin"},{"orcid":"0000-0003-4761-5996","first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"doi":"10.1016/j.devcel.2017.01.010","publist_id":"6320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","publication_status":"published","issue":"4","file":[{"file_size":6866187,"relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:10:57Z","creator":"system","content_type":"application/pdf","file_id":"4849","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_updated":"2018-12-12T10:10:57Z"}],"_id":"1067","day":"27","ec_funded":1,"pubrep_id":"869","oa":1,"ddc":["572","597"],"date_created":"2018-12-11T11:49:58Z","project":[{"grant_number":"201439","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-02-27T00:00:00Z","has_accepted_license":"1","scopus_import":"1","department":[{"_id":"CaHe"}],"isi":1,"type":"journal_article","status":"public","intvolume":"        40","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":40,"article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"file_date_updated":"2018-12-12T10:10:57Z","language":[{"iso":"eng"}],"page":"354 - 366","oa_version":"Published Version"}]