[{"title":"Rotation of quantum impurities in the presence of a many-body environment","isi":1,"article_number":"203001","date_updated":"2025-09-23T10:40:28Z","department":[{"_id":"MiLe"}],"month":"05","publication_status":"published","publisher":"American Physical Society","article_processing_charge":"No","doi":"10.1103/PhysRevLett.114.203001","year":"2015","date_published":"2015-05-18T00:00:00Z","citation":{"ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. 2015;114(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>.","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","apa":"Schmidt, R., &#38; Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” <i>Physical Review Letters</i>, vol. 114, no. 20. American Physical Society, 2015.","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001."},"abstract":[{"lang":"eng","text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system."}],"main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"quality_controlled":"1","external_id":{"isi":["000354969900003"],"arxiv":["1502.03447"]},"volume":114,"day":"18","oa_version":"Preprint","author":[{"last_name":"Schmidt","full_name":"Schmidt, Richard","first_name":"Richard"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","corr_author":"1","issue":"20","_id":"1813","arxiv":1,"oa":1,"intvolume":"       114","publist_id":"5293","publication":"Physical Review Letters","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:54:09Z","scopus_import":"1"},{"doi":"10.1145/2714572","publisher":"ACM","article_processing_charge":"No","publication_status":"published","citation":{"mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3, 27, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>.","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3. ACM, 2015.","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. 2015;34(3). doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>","apa":"Jeschke, S., &#38; Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015)."},"year":"2015","date_published":"2015-04-01T00:00:00Z","isi":1,"article_number":"27","title":"Water wave animation via wavefront parameter interpolation","month":"04","department":[{"_id":"ChWo"}],"date_updated":"2025-09-29T11:05:55Z","project":[{"grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","name":"Deep Pictures: Creating Visual and Haptic Vector Images","call_identifier":"FWF"},{"grant_number":"638176","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","external_id":{"isi":["000354800700004"]},"ec_funded":1,"pubrep_id":"575","day":"01","volume":34,"oa_version":"Submitted Version","abstract":[{"text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.","lang":"eng"}],"_id":"1814","oa":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"issue":"3","corr_author":"1","file_date_updated":"2020-07-14T12:45:17Z","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","has_accepted_license":"1","date_created":"2018-12-11T11:54:09Z","status":"public","scopus_import":"1","publist_id":"5292","intvolume":"        34","ddc":["000"],"file":[{"file_id":"4933","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":23712153,"date_created":"2018-12-12T10:12:15Z","checksum":"67c9f4fa370def68cdf31299e48bc91f"}]},{"date_updated":"2025-09-29T11:07:11Z","month":"03","department":[{"_id":"CaHe"}],"title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","isi":1,"year":"2015","date_published":"2015-03-16T00:00:00Z","citation":{"ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. 2015;521(7551):217-221. doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>.","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>","ieee":"S. Porazinski <i>et al.</i>, “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” <i>Nature</i>, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221."},"publication_status":"published","publisher":"Nature Publishing Group","article_processing_charge":"No","doi":"10.1038/nature14215","abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/","open_access":"1"}],"day":"16","volume":521,"oa_version":"Submitted Version","quality_controlled":"1","external_id":{"isi":["000354377800058"],"pmid":["25778702"]},"corr_author":"1","issue":"7551","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Porazinski","full_name":"Porazinski, Sean","first_name":"Sean"},{"first_name":"Huijia","last_name":"Wang","full_name":"Wang, Huijia"},{"last_name":"Asaoka","full_name":"Asaoka, Yoichi","first_name":"Yoichi"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin"},{"first_name":"Tatsuo","last_name":"Miyamoto","full_name":"Miyamoto, Tatsuo"},{"full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita","first_name":"Hitoshi"},{"last_name":"Hata","full_name":"Hata, Shoji","first_name":"Shoji"},{"first_name":"Takashi","full_name":"Sasaki, Takashi","last_name":"Sasaki"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"full_name":"Osada, Yumi","last_name":"Osada","first_name":"Yumi"},{"last_name":"Asaka","full_name":"Asaka, Satoshi","first_name":"Satoshi"},{"first_name":"Akihiro","full_name":"Momoi, Akihiro","last_name":"Momoi"},{"first_name":"Sarah","last_name":"Linton","full_name":"Linton, Sarah"},{"last_name":"Miesfeld","full_name":"Miesfeld, Joel","first_name":"Joel"},{"first_name":"Brian","last_name":"Link","full_name":"Link, Brian"},{"first_name":"Takeshi","full_name":"Senga, Takeshi","last_name":"Senga"},{"last_name":"Castillo Morales","full_name":"Castillo Morales, Atahualpa","first_name":"Atahualpa"},{"last_name":"Urrutia","full_name":"Urrutia, Araxi","first_name":"Araxi"},{"last_name":"Shimizu","full_name":"Shimizu, Nobuyoshi","first_name":"Nobuyoshi"},{"first_name":"Hideaki","last_name":"Nagase","full_name":"Nagase, Hideaki"},{"last_name":"Matsuura","full_name":"Matsuura, Shinya","first_name":"Shinya"},{"full_name":"Bagby, Stefan","last_name":"Bagby","first_name":"Stefan"},{"last_name":"Kondoh","full_name":"Kondoh, Hisato","first_name":"Hisato"},{"first_name":"Hiroshi","full_name":"Nishina, Hiroshi","last_name":"Nishina"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Furutani Seiki","full_name":"Furutani Seiki, Makoto","first_name":"Makoto"}],"type":"journal_article","oa":1,"_id":"1817","page":"217 - 221","intvolume":"       521","pmid":1,"publist_id":"5289","status":"public","date_created":"2018-12-11T11:54:10Z","scopus_import":"1","publication":"Nature","language":[{"iso":"eng"}]},{"year":"2015","date_published":"2015-05-19T00:00:00Z","citation":{"ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>."},"article_processing_charge":"No","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1421515112","publication_status":"published","date_updated":"2025-09-23T09:27:16Z","department":[{"_id":"NiBa"}],"month":"05","isi":1,"title":"Limits to adaptation along environmental gradients","ec_funded":1,"day":"19","volume":112,"oa_version":"Submitted Version","quality_controlled":"1","external_id":{"isi":["000354729500058"],"pmid":["25941385"]},"project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"oa":1,"_id":"1818","corr_author":"1","issue":"20","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"type":"journal_article","date_created":"2018-12-11T11:54:11Z","status":"public","scopus_import":"1","publication":"PNAS","language":[{"iso":"eng"}],"publist_id":"5288","intvolume":"       112","page":"6401 - 6406","pmid":1},{"type":"journal_article","author":[{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Jiřĺ","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","issue":"8","corr_author":"1","_id":"1819","publist_id":"5287","page":"1175 - 1187","intvolume":"         8","language":[{"iso":"eng"}],"publication":"Molecular Plant","date_created":"2018-12-11T11:54:11Z","scopus_import":"1","status":"public","isi":1,"title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","department":[{"_id":"JiFr"}],"month":"08","date_updated":"2025-09-23T09:47:17Z","doi":"10.1016/j.molp.2015.03.007","publisher":"Elsevier","article_processing_charge":"No","publication_status":"published","citation":{"apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., &#38; Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. 2015;8(8):1175-1187. doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>.","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” <i>Molecular Plant</i>, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015."},"date_published":"2015-08-03T00:00:00Z","year":"2015","abstract":[{"text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.","lang":"eng"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"external_id":{"isi":["000359136100006"]},"quality_controlled":"1","ec_funded":1,"volume":8,"day":"03","oa_version":"None"},{"isi":1,"title":"Optimal cost almost-sure reachability in POMDPs","date_updated":"2025-09-18T11:05:08Z","department":[{"_id":"KrCh"}],"month":"06","publisher":"AAAI Press","article_processing_charge":"No","publication_status":"published","date_published":"2015-06-01T00:00:00Z","year":"2015","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, vol. 5, AAAI Press, 2015, pp. 3496–502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i> (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>. Vol 5. AAAI Press; 2015:3496-3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, 5:3496–3502. AAAI Press, 2015."},"conference":{"end_date":"2015-01-30","name":"IAAI: Innovative Applications of Artificial Intelligence","start_date":"2015-01-25","location":"Austin, TX, USA"},"main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.","lang":"eng"}],"alternative_title":["Artifical Intelligence"],"quality_controlled":"1","external_id":{"arxiv":["1411.3880"],"isi":["000372683700002"]},"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"ec_funded":1,"day":"01","oa_version":"Preprint","volume":5,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"last_name":"Gupta","full_name":"Gupta, Raghav","first_name":"Raghav"},{"full_name":"Kanodia, Ayush","last_name":"Kanodia","first_name":"Ayush"}],"type":"conference","corr_author":"1","arxiv":1,"_id":"1820","related_material":{"record":[{"relation":"later_version","id":"1529","status":"public"}]},"oa":1,"publist_id":"5286","intvolume":"         5","page":"3496-3502","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:11Z","scopus_import":"1","status":"public"},{"file_date_updated":"2020-07-14T12:45:17Z","corr_author":"1","issue":"4","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","last_name":"Chevereau"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"}],"type":"journal_article","oa":1,"_id":"1823","file":[{"date_created":"2018-12-12T10:14:34Z","checksum":"4289b518fbe2166682fb1a1ef9b405f3","access_level":"open_access","relation":"main_file","file_size":1273573,"date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2015-395-v1+1_807.full.pdf","content_type":"application/pdf","creator":"system","file_id":"5087"}],"ddc":["570"],"intvolume":"        11","publist_id":"5283","date_created":"2018-12-11T11:54:12Z","scopus_import":"1","status":"public","has_accepted_license":"1","publication":"Molecular Systems Biology","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-09-23T13:38:00Z","month":"04","department":[{"_id":"ToBo"}],"title":"Systematic discovery of drug interaction mechanisms","isi":1,"article_number":"807","date_published":"2015-04-01T00:00:00Z","year":"2015","citation":{"short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","apa":"Chevereau, G., &#38; Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>","ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. 2015;11(4). doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” <i>Molecular Systems Biology</i>, vol. 11, no. 4. Nature Publishing Group, 2015.","mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>."},"publication_status":"published","publisher":"Nature Publishing Group","article_processing_charge":"No","doi":"10.15252/msb.20156098","abstract":[{"lang":"eng","text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways."}],"day":"01","oa_version":"Published Version","volume":11,"pubrep_id":"395","ec_funded":1,"external_id":{"isi":["000354022300005"]},"quality_controlled":"1","project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"},{"name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507"}]},{"publist_id":"5282","intvolume":"         6","ddc":["530"],"file":[{"date_created":"2018-12-12T10:16:54Z","checksum":"c4cffb5c8b245e658a34eac71a03e7cc","access_level":"open_access","file_size":1151501,"relation":"main_file","date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","content_type":"application/pdf","file_id":"5245","creator":"system"}],"language":[{"iso":"eng"}],"publication":"Nature Communications","has_accepted_license":"1","scopus_import":"1","date_created":"2018-12-11T11:54:13Z","status":"public","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Johannes","last_name":"Knebel","full_name":"Knebel, Johannes"},{"first_name":"Markus","last_name":"Weber","full_name":"Weber, Markus"},{"orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"},{"first_name":"Erwin","full_name":"Frey, Erwin","last_name":"Frey"}],"file_date_updated":"2020-07-14T12:45:17Z","_id":"1824","oa":1,"abstract":[{"lang":"eng","text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates."}],"external_id":{"isi":["000353705000003"]},"quality_controlled":"1","pubrep_id":"451","day":"24","oa_version":"Published Version","volume":6,"article_number":"6977","isi":1,"title":"Evolutionary games of condensates in coupled birth-death processes","department":[{"_id":"LaEr"}],"month":"04","date_updated":"2025-09-23T08:44:01Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.1038/ncomms7977","publisher":"Nature Publishing Group","article_processing_charge":"No","publication_status":"published","citation":{"ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>","chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","apa":"Knebel, J., Weber, M., Krüger, T. H., &#38; Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>, vol. 6, 6977, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>.","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977."},"date_published":"2015-04-24T00:00:00Z","year":"2015"},{"date_created":"2018-12-11T11:54:14Z","scopus_import":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"PLoS Computational Biology","file":[{"access_level":"open_access","relation":"main_file","file_size":1811647,"date_created":"2018-12-12T10:15:39Z","checksum":"b8aa66f450ff8de393014b87ec7d2efb","creator":"system","file_id":"5161","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf"}],"ddc":["576"],"intvolume":"        11","publist_id":"5278","related_material":{"record":[{"relation":"research_data","status":"public","id":"9718"},{"status":"public","id":"9773","relation":"research_data"}]},"oa":1,"_id":"1827","file_date_updated":"2020-07-14T12:45:17Z","issue":"3","type":"journal_article","author":[{"last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar","first_name":"Tamar"},{"last_name":"Mayo","full_name":"Mayo, Avraham","first_name":"Avraham"},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"last_name":"Alon","full_name":"Alon, Uri","first_name":"Uri"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"23","volume":11,"oa_version":"Published Version","pubrep_id":"452","ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","external_id":{"isi":["000352195700006"]},"abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"citation":{"ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” <i>PLoS Computational Biology</i>, vol. 11, no. 3. Public Library of Science, 2015.","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>, vol. 11, no. 3, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>.","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. 2015;11(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","apa":"Friedlander, T., Mayo, A., Tlusty, T., &#38; Alon, U. (2015). Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>"},"year":"2015","date_published":"2015-03-23T00:00:00Z","publication_status":"published","doi":"10.1371/journal.pcbi.1004055","publisher":"Public Library of Science","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"GaTk"}],"month":"03","date_updated":"2025-09-23T08:43:16Z","title":"Evolution of bow-tie architectures in biology","isi":1},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan"},{"last_name":"Pirogov","full_name":"Pirogov, Sergey","first_name":"Sergey"},{"last_name":"Rybko","full_name":"Rybko, Aleksandr","first_name":"Aleksandr"}],"type":"journal_article","corr_author":"1","issue":"1","_id":"1828","arxiv":1,"oa":1,"page":"163 - 167","intvolume":"       160","publist_id":"5276","publication":"Journal of Statistical Physics","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:54:14Z","scopus_import":"1","title":"Invariant measures of genetic recombination process","isi":1,"date_updated":"2025-09-23T09:23:53Z","department":[{"_id":"HeEd"}],"month":"07","publication_status":"published","article_processing_charge":"No","publisher":"Springer","doi":"10.1007/s10955-015-1238-5","date_published":"2015-07-01T00:00:00Z","year":"2015","citation":{"ista":"Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167.","mla":"Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” <i>Journal of Statistical Physics</i>, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:<a href=\"https://doi.org/10.1007/s10955-015-1238-5\">10.1007/s10955-015-1238-5</a>.","ieee":"A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” <i>Journal of Statistical Physics</i>, vol. 160, no. 1. Springer, pp. 163–167, 2015.","apa":"Akopyan, A., Pirogov, S., &#38; Rybko, A. (2015). Invariant measures of genetic recombination process. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-015-1238-5\">https://doi.org/10.1007/s10955-015-1238-5</a>","short":"A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167.","chicago":"Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” <i>Journal of Statistical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10955-015-1238-5\">https://doi.org/10.1007/s10955-015-1238-5</a>.","ama":"Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. <i>Journal of Statistical Physics</i>. 2015;160(1):163-167. doi:<a href=\"https://doi.org/10.1007/s10955-015-1238-5\">10.1007/s10955-015-1238-5</a>"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1406.5313","open_access":"1"}],"abstract":[{"lang":"eng","text":"We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory."}],"external_id":{"arxiv":["1406.5313"],"isi":["000356579000009"]},"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"day":"01","volume":160,"oa_version":"Preprint","ec_funded":1},{"external_id":{"isi":["000354143400010"],"pmid":["25870394"]},"quality_controlled":"1","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"243071"},{"call_identifier":"FP7","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","grant_number":"302004"},{"_id":"25E0E184-B435-11E9-9278-68D0E5697425","name":"Schnellboot Antnet Junge Akademie"},{"name":"Fellowship of Wissenschaftskolleg zu Berlin","_id":"25E24DB2-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa_version":"Submitted Version","volume":370,"day":"26","article_type":"original","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/"}],"publisher":"Royal Society, The","article_processing_charge":"No","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"doi":"10.1098/rstb.2014.0108","publication_status":"published","year":"2015","date_published":"2015-05-26T00:00:00Z","citation":{"short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","apa":"Theis, F., Ugelvig, L. V., Marr, C., &#38; Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2014.0108\">https://doi.org/10.1098/rstb.2014.0108</a>","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2015;370(1669). doi:<a href=\"https://doi.org/10.1098/rstb.2014.0108\">10.1098/rstb.2014.0108</a>","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2015. <a href=\"https://doi.org/10.1098/rstb.2014.0108\">https://doi.org/10.1098/rstb.2014.0108</a>.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669. Royal Society, The, 2015.","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669, Royal Society, The, 2015, doi:<a href=\"https://doi.org/10.1098/rstb.2014.0108\">10.1098/rstb.2014.0108</a>."},"isi":1,"title":"Opposing effects of allogrooming on disease transmission in ant societies","date_updated":"2025-09-23T09:44:53Z","month":"05","department":[{"_id":"SyCr"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:54:15Z","scopus_import":"1","publist_id":"5273","intvolume":"       370","pmid":1,"_id":"1830","related_material":{"record":[{"status":"public","id":"9721","relation":"research_data"}]},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Theis, Fabian","last_name":"Theis","first_name":"Fabian"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","type":"journal_article","corr_author":"1","issue":"1669"},{"date_updated":"2025-09-23T10:46:39Z","department":[{"_id":"SyCr"}],"month":"05","article_number":"20140116","isi":1,"title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","date_published":"2015-05-01T00:00:00Z","year":"2015","citation":{"chicago":"Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rstb.2014.0116\">https://doi.org/10.1098/rstb.2014.0116</a>.","ama":"Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2015;370(1669). doi:<a href=\"https://doi.org/10.1098/rstb.2014.0116\">10.1098/rstb.2014.0116</a>","apa":"Kappeler, P., Cremer, S., &#38; Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2014.0116\">https://doi.org/10.1098/rstb.2014.0116</a>","short":"P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","mla":"Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rstb.2014.0116\">10.1098/rstb.2014.0116</a>.","ieee":"P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669. Royal Society, 2015.","ista":"Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116."},"publisher":"Royal Society","article_processing_charge":"No","doi":"10.1098/rstb.2014.0116","publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/","open_access":"1"}],"abstract":[{"text":"This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.","lang":"eng"}],"day":"01","oa_version":"Submitted Version","volume":370,"quality_controlled":"1","external_id":{"pmid":["25870402"],"isi":["000354143400001"]},"issue":"1669","acknowledgement":"We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Peter","full_name":"Kappeler, Peter","last_name":"Kappeler"},{"orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charles","full_name":"Nunn, Charles","last_name":"Nunn"}],"type":"journal_article","oa":1,"_id":"1831","publist_id":"5272","pmid":1,"intvolume":"       370","date_created":"2018-12-11T11:54:15Z","status":"public","scopus_import":"1","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication":"Logical Methods in Computer Science","has_accepted_license":"1","status":"public","scopus_import":"1","date_created":"2018-12-11T11:54:15Z","publist_id":"5271","intvolume":"        11","ddc":["000"],"file":[{"checksum":"7370e164d0a731f442424a92669efc34","date_created":"2018-12-12T10:11:27Z","file_size":380203,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-390-v1+1_1502.07639.pdf","date_updated":"2020-07-14T12:45:17Z","creator":"system","file_id":"4881"}],"_id":"1832","oa":1,"related_material":{"record":[{"relation":"earlier_version","id":"2328","status":"public"}]},"type":"journal_article","author":[{"full_name":"Chakraborty, Soham","last_name":"Chakraborty","first_name":"Soham"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali"},{"first_name":"Viktor","last_name":"Vafeiadis","full_name":"Vafeiadis, Viktor"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1","corr_author":"1","file_date_updated":"2020-07-14T12:45:17Z","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"external_id":{"isi":["000353193000019"]},"quality_controlled":"1","ec_funded":1,"pubrep_id":"390","day":"01","volume":11,"oa_version":"Published Version","article_type":"original","abstract":[{"text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on the identification of the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof. ","lang":"eng"}],"doi":"10.2168/LMCS-11(1:20)2015","article_processing_charge":"No","publisher":"International Federation of Computational Logic","publication_status":"published","citation":{"ama":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. <i>Logical Methods in Computer Science</i>. 2015;11(1). doi:<a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">10.2168/LMCS-11(1:20)2015</a>","chicago":"Chakraborty, Soham, Thomas A Henzinger, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2015. <a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">https://doi.org/10.2168/LMCS-11(1:20)2015</a>.","short":"S. Chakraborty, T.A. Henzinger, A. Sezgin, V. Vafeiadis, Logical Methods in Computer Science 11 (2015).","apa":"Chakraborty, S., Henzinger, T. A., Sezgin, A., &#38; Vafeiadis, V. (2015). Aspect-oriented linearizability proofs. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">https://doi.org/10.2168/LMCS-11(1:20)2015</a>","ieee":"S. Chakraborty, T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” <i>Logical Methods in Computer Science</i>, vol. 11, no. 1. International Federation of Computational Logic, 2015.","mla":"Chakraborty, Soham, et al. “Aspect-Oriented Linearizability Proofs.” <i>Logical Methods in Computer Science</i>, vol. 11, no. 1, 20, International Federation of Computational Logic, 2015, doi:<a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">10.2168/LMCS-11(1:20)2015</a>.","ista":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 11(1), 20."},"year":"2015","date_published":"2015-04-01T00:00:00Z","isi":1,"article_number":"20","title":"Aspect-oriented linearizability proofs","month":"04","department":[{"_id":"ToHe"}],"date_updated":"2025-09-23T07:56:20Z","tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nd/4.0/"},{"license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"date_updated":"2025-09-23T09:31:50Z","department":[{"_id":"PeJo"}],"month":"04","title":"Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats","isi":1,"year":"2015","date_published":"2015-04-13T00:00:00Z","citation":{"ista":"Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2).","mla":"Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” <i>ASN Neuro</i>, vol. 7, no. 2, SAGE Publications, 2015, doi:<a href=\"https://doi.org/10.1177/1759091415575845\">10.1177/1759091415575845</a>.","ieee":"C. Chen <i>et al.</i>, “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” <i>ASN Neuro</i>, vol. 7, no. 2. SAGE Publications, 2015.","apa":"Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., &#38; Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. <i>ASN Neuro</i>. SAGE Publications. <a href=\"https://doi.org/10.1177/1759091415575845\">https://doi.org/10.1177/1759091415575845</a>","short":"C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015).","chicago":"Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” <i>ASN Neuro</i>. SAGE Publications, 2015. <a href=\"https://doi.org/10.1177/1759091415575845\">https://doi.org/10.1177/1759091415575845</a>.","ama":"Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. <i>ASN Neuro</i>. 2015;7(2). doi:<a href=\"https://doi.org/10.1177/1759091415575845\">10.1177/1759091415575845</a>"},"publication_status":"published","publisher":"SAGE Publications","article_processing_charge":"No","doi":"10.1177/1759091415575845","abstract":[{"lang":"eng","text":"Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks."}],"article_type":"original","volume":7,"day":"13","oa_version":"Published Version","pubrep_id":"456","external_id":{"isi":["000353223200002"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:18Z","issue":"2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Chong","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"last_name":"Wang","full_name":"Wang, Chao","first_name":"Chao"},{"last_name":"Zhao","full_name":"Zhao, Xuan","first_name":"Xuan"},{"last_name":"Zhou","full_name":"Zhou, Tao","first_name":"Tao"},{"last_name":"Xu","full_name":"Xu, Dao","first_name":"Dao"},{"full_name":"Wang, Zhi","last_name":"Wang","first_name":"Zhi"},{"last_name":"Wang","full_name":"Wang, Ying","first_name":"Ying"}],"type":"journal_article","oa":1,"_id":"1834","file":[{"relation":"main_file","file_size":1146814,"access_level":"open_access","checksum":"53e16bd3fc2ae2c0d7de9164626c37aa","date_created":"2018-12-12T10:14:08Z","creator":"system","file_id":"5057","content_type":"application/pdf","file_name":"IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf","date_updated":"2020-07-14T12:45:18Z"}],"ddc":["570"],"intvolume":"         7","publist_id":"5269","date_created":"2018-12-11T11:54:16Z","status":"public","scopus_import":"1","has_accepted_license":"1","publication":"ASN Neuro","language":[{"iso":"eng"}]},{"main_file_link":[{"url":"http://arxiv.org/abs/1410.7704","open_access":"1"}],"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 logics. 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."}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11"},"ec_funded":1,"volume":9035,"oa_version":"Preprint","day":"01","alternative_title":["LNCS"],"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"quality_controlled":"1","external_id":{"arxiv":["1410.7704"]},"month":"04","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"date_updated":"2025-07-10T11:50:42Z","title":"Model checking gene regulatory networks","citation":{"short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","mla":"Giacobbe, Mirco, et al. <i>Model Checking Gene Regulatory Networks</i>. Vol. 9035, Springer, 2015, pp. 469–83, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>."},"date_published":"2015-04-01T00:00:00Z","year":"2015","doi":"10.1007/978-3-662-46681-0_47","article_processing_charge":"No","publisher":"Springer","publication_status":"published","series_title":"Lecture Notes in Computer Science","publist_id":"5267","intvolume":"      9035","page":"469 - 483","date_created":"2018-12-11T11:54:16Z","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"type":"conference","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","author":[{"first_name":"Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052"},{"last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","status":"public","id":"1351"}]},"oa":1,"arxiv":1,"_id":"1835"},{"abstract":[{"lang":"eng","text":"In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools."}],"conference":{"location":"London, United Kingdom","start_date":"2015-04-11","name":"ESOP: European Symposium on Programming","end_date":"2015-04-18"},"oa_version":"None","day":"01","volume":9032,"ec_funded":1,"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}],"quality_controlled":"1","external_id":{"isi":["000361751400005"]},"alternative_title":["LNCS"],"department":[{"_id":"ToHe"}],"month":"04","date_updated":"2025-09-23T10:42:04Z","title":"Segment abstraction for worst-case execution time analysis","isi":1,"citation":{"ieee":"P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr, “Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer, pp. 105–131, 2015.","mla":"Cerny, Pavol, et al. <i>Segment Abstraction for Worst-Case Execution Time Analysis</i>. Vol. 9032, Springer, 2015, pp. 105–31, doi:<a href=\"https://doi.org/10.1007/978-3-662-46669-8_5\">10.1007/978-3-662-46669-8_5</a>.","ista":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131.","ama":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction for worst-case execution time analysis. 2015;9032:105-131. doi:<a href=\"https://doi.org/10.1007/978-3-662-46669-8_5\">10.1007/978-3-662-46669-8_5</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46669-8_5\">https://doi.org/10.1007/978-3-662-46669-8_5</a>.","short":"P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131.","apa":"Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., &#38; Zwirchmayr, J. (2015). Segment abstraction for worst-case execution time analysis. Presented at the ESOP: European Symposium on Programming, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46669-8_5\">https://doi.org/10.1007/978-3-662-46669-8_5</a>"},"year":"2015","date_published":"2015-04-01T00:00:00Z","publication_status":"published","doi":"10.1007/978-3-662-46669-8_5","article_processing_charge":"No","publisher":"Springer","series_title":"Lecture Notes in Computer Science","intvolume":"      9032","page":"105 - 131","publist_id":"5266","date_created":"2018-12-11T11:54:16Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"type":"conference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun"},{"last_name":"Zwirchmayr","full_name":"Zwirchmayr, Jakob","first_name":"Jakob"}],"_id":"1836"},{"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","full_name":"Kühnen, Jakob","last_name":"Kühnen","first_name":"Jakob","orcid":"0000-0003-4312-0179"},{"full_name":"Braunshier, P","last_name":"Braunshier","first_name":"P"},{"first_name":"M","last_name":"Schwegel","full_name":"Schwegel, M"},{"last_name":"Kuhlmann","full_name":"Kuhlmann, Hendrik","first_name":"Hendrik"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"issue":"5","corr_author":"1","arxiv":1,"_id":"1837","oa":1,"publist_id":"5265","intvolume":"       770","language":[{"iso":"eng"}],"publication":"Journal of Fluid Mechanics","date_created":"2018-12-11T11:54:17Z","status":"public","scopus_import":"1","isi":1,"article_number":"R3","title":"Subcritical versus supercritical transition to turbulence in curved pipes","department":[{"_id":"BjHo"}],"month":"04","date_updated":"2025-09-23T10:50:18Z","doi":"10.1017/jfm.2015.184","publisher":"Cambridge University Press","article_processing_charge":"No","publication_status":"published","citation":{"ista":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3.","mla":"Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” <i>Journal of Fluid Mechanics</i>, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:<a href=\"https://doi.org/10.1017/jfm.2015.184\">10.1017/jfm.2015.184</a>.","ieee":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” <i>Journal of Fluid Mechanics</i>, vol. 770, no. 5. Cambridge University Press, 2015.","apa":"Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., &#38; Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2015.184\">https://doi.org/10.1017/jfm.2015.184</a>","short":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015).","chicago":"Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2015. <a href=\"https://doi.org/10.1017/jfm.2015.184\">https://doi.org/10.1017/jfm.2015.184</a>.","ama":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. <i>Journal of Fluid Mechanics</i>. 2015;770(5). doi:<a href=\"https://doi.org/10.1017/jfm.2015.184\">10.1017/jfm.2015.184</a>"},"date_published":"2015-04-08T00:00:00Z","year":"2015","article_type":"original","abstract":[{"text":"Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06559"}],"project":[{"name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"306589"}],"quality_controlled":"1","external_id":{"isi":["000354190500003"],"arxiv":["1508.06559"]},"ec_funded":1,"day":"08","oa_version":"Preprint","volume":770},{"external_id":{"arxiv":["1411.4604"]},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"alternative_title":["LNCS"],"volume":9035,"oa_version":"Preprint","day":"01","ec_funded":1,"conference":{"end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11","location":"London, United Kingdom"},"abstract":[{"text":"Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples.","lang":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1411.4604","open_access":"1"}],"publication_status":"published","article_processing_charge":"No","publisher":"Springer","doi":"10.1007/978-3-662-46681-0_50","date_published":"2015-01-01T00:00:00Z","year":"2015","citation":{"ista":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.","mla":"Bloem, Roderick, et al. <i>Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information</i>. Vol. 9035, Springer, 2015, pp. 517–32, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">10.1007/978-3-662-46681-0_50</a>.","ieee":"R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.","apa":"Bloem, R., Chatterjee, K., Jacobs, S., &#38; Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">https://doi.org/10.1007/978-3-662-46681-0_50</a>","short":"R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">https://doi.org/10.1007/978-3-662-46681-0_50</a>.","ama":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">10.1007/978-3-662-46681-0_50</a>"},"title":"Assume-guarantee synthesis for concurrent reactive programs with partial information","date_updated":"2025-06-11T07:09:03Z","department":[{"_id":"KrCh"}],"month":"01","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:17Z","status":"public","scopus_import":"1","intvolume":"      9035","page":"517 - 532","publist_id":"5264","_id":"1838","arxiv":1,"oa":1,"author":[{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Swen","last_name":"Jacobs","full_name":"Jacobs, Swen"},{"first_name":"Robert","last_name":"Könighofer","full_name":"Könighofer, Robert"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference"},{"oa":1,"_id":"1839","arxiv":1,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"}],"scopus_import":"1","date_created":"2018-12-11T11:54:18Z","status":"public","language":[{"iso":"eng"}],"series_title":"Lecture Notes in Computer Science","intvolume":"      9035","page":"181 - 187","publist_id":"5263","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">https://doi.org/10.1007/978-3-662-46681-0_12</a>.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">10.1007/978-3-662-46681-0_12</a>","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">https://doi.org/10.1007/978-3-662-46681-0_12</a>","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187.","mla":"Brázdil, Tomáš, et al. <i>Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives</i>. Vol. 9035, Springer, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">10.1007/978-3-662-46681-0_12</a>.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187."},"date_published":"2015-01-01T00:00:00Z","year":"2015","publication_status":"published","doi":"10.1007/978-3-662-46681-0_12","article_processing_charge":"No","publisher":"Springer","department":[{"_id":"KrCh"}],"month":"01","date_updated":"2025-06-11T07:09:21Z","title":"Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives","day":"01","oa_version":"Preprint","volume":9035,"ec_funded":1,"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"external_id":{"arxiv":["1501.03093"]},"quality_controlled":"1","alternative_title":["LNCS"],"abstract":[{"text":"We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies.","lang":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1501.03093","open_access":"1"}],"conference":{"location":"London, United Kingdom","start_date":"2015-04-11","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2015-04-18"}},{"oa":1,"_id":"1840","arxiv":1,"issue":"4","author":[{"first_name":"Bernhard","last_name":"Geiger","full_name":"Geiger, Bernhard"},{"first_name":"Tatjana","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov"},{"last_name":"Kubin","full_name":"Kubin, Gernot","first_name":"Gernot"},{"first_name":"Heinz","last_name":"Koeppl","full_name":"Koeppl, Heinz"}],"acknowledgement":"This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","date_created":"2018-12-11T11:54:18Z","scopus_import":"1","status":"public","publication":"IEEE Transactions on Automatic Control","language":[{"iso":"eng"}],"intvolume":"        60","page":"1010 - 1022","publist_id":"5262","date_published":"2015-04-01T00:00:00Z","year":"2015","citation":{"apa":"Geiger, B., Petrov, T., Kubin, G., &#38; Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. <i>IEEE Transactions on Automatic Control</i>. IEEE. <a href=\"https://doi.org/10.1109/TAC.2014.2364971\">https://doi.org/10.1109/TAC.2014.2364971</a>","short":"B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.","chicago":"Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” <i>IEEE Transactions on Automatic Control</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TAC.2014.2364971\">https://doi.org/10.1109/TAC.2014.2364971</a>.","ama":"Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. <i>IEEE Transactions on Automatic Control</i>. 2015;60(4):1010-1022. doi:<a href=\"https://doi.org/10.1109/TAC.2014.2364971\">10.1109/TAC.2014.2364971</a>","ista":"Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022.","mla":"Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” <i>IEEE Transactions on Automatic Control</i>, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:<a href=\"https://doi.org/10.1109/TAC.2014.2364971\">10.1109/TAC.2014.2364971</a>.","ieee":"B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” <i>IEEE Transactions on Automatic Control</i>, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015."},"publication_status":"published","article_processing_charge":"No","publisher":"IEEE","publication_identifier":{"issn":["0018-9286"]},"doi":"10.1109/TAC.2014.2364971","date_updated":"2025-09-23T09:45:33Z","month":"04","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"title":"Optimal Kullback-Leibler aggregation via information bottleneck","isi":1,"day":"01","volume":60,"oa_version":"Preprint","quality_controlled":"1","external_id":{"isi":["000351731600009"],"arxiv":["1304.6603"]},"main_file_link":[{"url":"http://arxiv.org/abs/1304.6603","open_access":"1"}],"abstract":[{"text":"In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.","lang":"eng"}]}]