[{"conference":{"location":"Toronto, Canada","start_date":"2016-07-17","end_date":"2016-07-23","name":"CAV: Computer Aided Verification"},"date_updated":"2025-09-22T07:30:07Z","month":"07","isi":1,"page":"383 - 401","author":[{"full_name":"D'Antoni, Loris","first_name":"Loris","last_name":"D'Antoni"},{"full_name":"Samanta, Roopsha","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta"},{"last_name":"Singh","first_name":"Rishabh","full_name":"Singh, Rishabh"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"scopus_import":"1","date_created":"2018-12-11T11:51:45Z","volume":9780,"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000387731400021"]},"publist_id":"5819","citation":{"apa":"D’Antoni, L., Samanta, R., & Singh, R. (2016). QLOSE: Program repair with quantitative objectives (Vol. 9780, pp. 383–401). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_21","mla":"D’Antoni, Loris, et al. QLOSE: Program Repair with Quantitative Objectives. Vol. 9780, Springer, 2016, pp. 383–401, doi:10.1007/978-3-319-41540-6_21.","ieee":"L. D’Antoni, R. Samanta, and R. Singh, “QLOSE: Program repair with quantitative objectives,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 383–401.","ista":"D’Antoni L, Samanta R, Singh R. 2016. QLOSE: Program repair with quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 9780, 383–401.","ama":"D’Antoni L, Samanta R, Singh R. QLOSE: Program repair with quantitative objectives. In: Vol 9780. Springer; 2016:383-401. doi:10.1007/978-3-319-41540-6_21","chicago":"D’Antoni, Loris, Roopsha Samanta, and Rishabh Singh. “QLOSE: Program Repair with Quantitative Objectives,” 9780:383–401. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_21.","short":"L. D’Antoni, R. Samanta, R. Singh, in:, Springer, 2016, pp. 383–401."},"year":"2016","oa_version":"None","doi":"10.1007/978-3-319-41540-6_21","publisher":"Springer","corr_author":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"The goal of automatic program repair is to identify a set of syntactic changes that can turn a program that is incorrect with respect\r\nto a given specification into a correct one. Existing program repair techniques typically aim to find any program that meets the given specification. Such “best-effort” strategies can end up generating a program that is quite different from the original one. Novel techniques have been proposed to compute syntactically minimal program fixes, but the smallest syntactic fix to a program can still significantly alter the original program’s behaviour. We propose a new approach to program repair based on program distances, which can quantify changes not only to the program syntax but also to the program semantics. We call this the quantitative program repair problem where the “optimal” repair is derived using multiple distances. We implement a solution to the quantitative repair\r\nproblem in a prototype tool called Qlose\r\n(Quantitatively close), using the program synthesizer Sketch. We evaluate the effectiveness of different distances in obtaining desirable repairs by evaluating\r\nQlose on programs taken from educational tools such as CodeHunt and edX.","lang":"eng"}],"_id":"1390","department":[{"_id":"ToHe"}],"day":"13","title":"QLOSE: Program repair with quantitative objectives","ec_funded":1,"intvolume":" 9780","status":"public","article_processing_charge":"No","alternative_title":["LNCS"],"date_published":"2016-07-13T00:00:00Z","type":"conference"},{"volume":13,"issue":"3","scopus_import":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_created":"2018-12-11T11:51:46Z","author":[{"last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"},{"last_name":"Capuani","first_name":"Fabrizio","full_name":"Capuani, Fabrizio"},{"last_name":"De Martino","first_name":"Andrea","full_name":"De Martino, Andrea"}],"date_updated":"2025-09-18T14:31:33Z","month":"05","isi":1,"publication":"Physical Biology","year":"2016","citation":{"ama":"De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005","ista":"De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing, 2016.","mla":"De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing, 2016, doi:10.1088/1478-3975/13/3/036005.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing, 2016. https://doi.org/10.1088/1478-3975/13/3/036005.","apa":"De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing. https://doi.org/10.1088/1478-3975/13/3/036005"},"publist_id":"5815","external_id":{"arxiv":["1601.03243"],"isi":["000380148200014"]},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"text":"The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity.","lang":"eng"}],"quality_controlled":"1","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"IOP Publishing","oa":1,"article_number":"036005","doi":"10.1088/1478-3975/13/3/036005","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1601.03243","open_access":"1"}],"date_published":"2016-05-27T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","intvolume":" 13","ec_funded":1,"day":"27","title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","_id":"1394","department":[{"_id":"GaTk"}],"acknowledgement":"The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038."},{"_id":"14010","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"intvolume":" 117","day":"26","title":"Attosecond delays in molecular photoionization","article_processing_charge":"No","status":"public","extern":"1","date_published":"2016-08-26T00:00:00Z","type":"journal_article","doi":"10.1103/physrevlett.117.093001","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.07435"}],"oa":1,"article_number":"093001","arxiv":1,"quality_controlled":"1","keyword":["General Physics and Astronomy"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"We report measurements of energy-dependent attosecond photoionization delays between the two outer-most valence shells of N2O and H2O. The combination of single-shot signal referencing with the use of different metal foils to filter the attosecond pulse train enables us to extract delays from congested spectra. Remarkably large delays up to 160 as are observed in N2O, whereas the delays in H2O are all smaller than 50 as in the photon-energy range of 20-40 eV. These results are interpreted by developing a theory of molecular photoionization delays. The long delays measured in N2O are shown to reflect the population of molecular shape resonances that trap the photoelectron for a duration of up to ∼110 as. The unstructured continua of H2O result in much smaller delays at the same photon energies. Our experimental and theoretical methods make the study of molecular attosecond photoionization dynamics accessible."}],"pmid":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1607.07435"],"pmid":["27610849"]},"publication_status":"published","citation":{"apa":"Huppert, M., Jordan, I., Baykusheva, D. R., von Conta, A., & Wörner, H. J. (2016). Attosecond delays in molecular photoionization. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.117.093001","chicago":"Huppert, Martin, Inga Jordan, Denitsa Rangelova Baykusheva, Aaron von Conta, and Hans Jakob Wörner. “Attosecond Delays in Molecular Photoionization.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/physrevlett.117.093001.","short":"M. Huppert, I. Jordan, D.R. Baykusheva, A. von Conta, H.J. Wörner, Physical Review Letters 117 (2016).","mla":"Huppert, Martin, et al. “Attosecond Delays in Molecular Photoionization.” Physical Review Letters, vol. 117, no. 9, 093001, American Physical Society, 2016, doi:10.1103/physrevlett.117.093001.","ieee":"M. Huppert, I. Jordan, D. R. Baykusheva, A. von Conta, and H. J. Wörner, “Attosecond delays in molecular photoionization,” Physical Review Letters, vol. 117, no. 9. American Physical Society, 2016.","ista":"Huppert M, Jordan I, Baykusheva DR, von Conta A, Wörner HJ. 2016. Attosecond delays in molecular photoionization. Physical Review Letters. 117(9), 093001.","ama":"Huppert M, Jordan I, Baykusheva DR, von Conta A, Wörner HJ. Attosecond delays in molecular photoionization. Physical Review Letters. 2016;117(9). doi:10.1103/physrevlett.117.093001"},"publication":"Physical Review Letters","year":"2016","date_updated":"2023-08-22T08:42:50Z","month":"08","author":[{"first_name":"Martin","last_name":"Huppert","full_name":"Huppert, Martin"},{"full_name":"Jordan, Inga","first_name":"Inga","last_name":"Jordan"},{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"last_name":"von Conta","first_name":"Aaron","full_name":"von Conta, Aaron"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"article_type":"original","volume":117,"scopus_import":"1","issue":"9","date_created":"2023-08-10T06:37:07Z"},{"month":"03","date_updated":"2023-08-22T08:44:10Z","volume":116,"date_created":"2023-08-10T06:37:16Z","issue":"12","scopus_import":"1","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Ahsan, Md Sabbir","last_name":"Ahsan","first_name":"Md Sabbir"},{"full_name":"Lin, Nan","last_name":"Lin","first_name":"Nan"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"article_type":"original","external_id":{"pmid":["27058077"]},"publication_status":"published","language":[{"iso":"eng"}],"publication":"Physical Review Letters","year":"2016","citation":{"short":"D.R. Baykusheva, M.S. Ahsan, N. Lin, H.J. Wörner, Physical Review Letters 116 (2016).","chicago":"Baykusheva, Denitsa Rangelova, Md Sabbir Ahsan, Nan Lin, and Hans Jakob Wörner. “Bicircular High-Harmonic Spectroscopy Reveals Dynamical Symmetries of Atoms and Molecules.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/physrevlett.116.123001.","ista":"Baykusheva DR, Ahsan MS, Lin N, Wörner HJ. 2016. Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules. Physical Review Letters. 116(12), 123001.","ama":"Baykusheva DR, Ahsan MS, Lin N, Wörner HJ. Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules. Physical Review Letters. 2016;116(12). doi:10.1103/physrevlett.116.123001","ieee":"D. R. Baykusheva, M. S. Ahsan, N. Lin, and H. J. Wörner, “Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules,” Physical Review Letters, vol. 116, no. 12. American Physical Society, 2016.","mla":"Baykusheva, Denitsa Rangelova, et al. “Bicircular High-Harmonic Spectroscopy Reveals Dynamical Symmetries of Atoms and Molecules.” Physical Review Letters, vol. 116, no. 12, 123001, American Physical Society, 2016, doi:10.1103/physrevlett.116.123001.","apa":"Baykusheva, D. R., Ahsan, M. S., Lin, N., & Wörner, H. J. (2016). Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.116.123001"},"article_number":"123001","doi":"10.1103/physrevlett.116.123001","oa_version":"None","abstract":[{"lang":"eng","text":"We introduce bicircular high-harmonic spectroscopy as a new method to probe dynamical symmetries of atoms and molecules and their evolution in time. Our approach is based on combining a circularly polarized femtosecond fundamental field of frequency ω with its counterrotating second harmonic 2ω. We demonstrate the ability of bicircular high-harmonic spectroscopy to characterize the orbital angular momentum symmetry of atomic orbitals. We further show that breaking the threefold rotational symmetry of the generating medium-at the level of either the ensemble or that of a single molecule-results in the emission of the otherwise parity-forbidden frequencies 3qω  (q∈N), which provide a background-free probe of dynamical molecular symmetries."}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Physics and Astronomy"],"quality_controlled":"1","publisher":"American Physical Society","intvolume":" 116","title":"Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules","day":"25","_id":"14011","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"type":"journal_article","date_published":"2016-03-25T00:00:00Z","article_processing_charge":"No","extern":"1","status":"public"},{"date_updated":"2023-08-22T08:46:05Z","month":"11","scopus_import":"1","issue":"11","date_created":"2023-08-10T06:37:25Z","volume":5,"article_type":"original","page":"e16170-e16170","author":[{"full_name":"Rajeev, Rajendran","first_name":"Rajendran","last_name":"Rajeev"},{"full_name":"Hellwagner, Johannes","first_name":"Johannes","last_name":"Hellwagner"},{"full_name":"Schumacher, Anne","first_name":"Anne","last_name":"Schumacher"},{"full_name":"Jordan, Inga","last_name":"Jordan","first_name":"Inga"},{"last_name":"Huppert","first_name":"Martin","full_name":"Huppert, Martin"},{"last_name":"Tehlar","first_name":"Andres","full_name":"Tehlar, Andres"},{"last_name":"Niraghatam","first_name":"Bhargava Ram","full_name":"Niraghatam, Bhargava Ram"},{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"first_name":"Nan","last_name":"Lin","full_name":"Lin, Nan"},{"full_name":"von Conta, Aaron","first_name":"Aaron","last_name":"von Conta"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"publication_status":"published","external_id":{"pmid":["30167130"]},"language":[{"iso":"eng"}],"year":"2016","publication":"Light: Science & Applications","citation":{"apa":"Rajeev, R., Hellwagner, J., Schumacher, A., Jordan, I., Huppert, M., Tehlar, A., … Wörner, H. J. (2016). In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses. Light: Science & Applications. Springer Nature. https://doi.org/10.1038/lsa.2016.170","mla":"Rajeev, Rajendran, et al. “In Situ Frequency Gating and Beam Splitting of Vacuum- and Extreme-Ultraviolet Pulses.” Light: Science & Applications, vol. 5, no. 11, Springer Nature, 2016, pp. e16170–e16170, doi:10.1038/lsa.2016.170.","ieee":"R. Rajeev et al., “In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses,” Light: Science & Applications, vol. 5, no. 11. Springer Nature, pp. e16170–e16170, 2016.","ista":"Rajeev R, Hellwagner J, Schumacher A, Jordan I, Huppert M, Tehlar A, Niraghatam BR, Baykusheva DR, Lin N, von Conta A, Wörner HJ. 2016. In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses. Light: Science & Applications. 5(11), e16170–e16170.","ama":"Rajeev R, Hellwagner J, Schumacher A, et al. In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses. Light: Science & Applications. 2016;5(11):e16170-e16170. doi:10.1038/lsa.2016.170","chicago":"Rajeev, Rajendran, Johannes Hellwagner, Anne Schumacher, Inga Jordan, Martin Huppert, Andres Tehlar, Bhargava Ram Niraghatam, et al. “In Situ Frequency Gating and Beam Splitting of Vacuum- and Extreme-Ultraviolet Pulses.” Light: Science & Applications. Springer Nature, 2016. https://doi.org/10.1038/lsa.2016.170.","short":"R. Rajeev, J. Hellwagner, A. Schumacher, I. Jordan, M. Huppert, A. Tehlar, B.R. Niraghatam, D.R. Baykusheva, N. Lin, A. von Conta, H.J. Wörner, Light: Science & Applications 5 (2016) e16170–e16170."},"oa":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1038/lsa.2016.170","open_access":"1"}],"doi":"10.1038/lsa.2016.170","pmid":1,"abstract":[{"text":"Monochromatization of high-harmonic sources has opened fascinating perspectives regarding time-resolved photoemission from all phases of matter. Such studies have invariably involved the use of spectral filters or spectrally dispersive optical components that are inherently lossy and technically complex. Here we present a new technique for the spectral selection of near-threshold harmonics and their spatial separation from the driving beams without any optical elements. We discover the existence of a narrow phase-matching gate resulting from the combination of the non-collinear generation geometry in an extended medium, atomic resonances and absorption. Our technique offers a filter contrast of up to 104 for the selected harmonics against the adjacent ones and offers multiple temporally synchronized beamlets in a single unified scheme. We demonstrate the selective generation of 133, 80 or 56 nm femtosecond pulses from a 400-nm driver, which is specific to the target gas. These results open new pathways towards phase-sensitive multi-pulse spectroscopy in the vacuum- and extreme-ultraviolet, and frequency-selective output coupling from enhancement cavities.","lang":"eng"}],"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Atomic and Molecular Physics","and Optics","Electronic","Optical and Magnetic Materials"],"day":"01","title":"In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses","intvolume":" 5","publication_identifier":{"eissn":["2047-7538"]},"_id":"14012","date_published":"2016-11-01T00:00:00Z","type":"journal_article","status":"public","extern":"1","article_processing_charge":"No"},{"isi":1,"month":"07","date_updated":"2025-09-18T14:30:52Z","file_date_updated":"2020-07-14T12:44:53Z","page":"126 - 164","author":[{"full_name":"Franek, Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8878-8397","first_name":"Peter"},{"full_name":"Krcál, Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"}],"date_created":"2018-12-11T11:51:51Z","file":[{"file_size":905303,"date_updated":"2020-07-14T12:44:53Z","creator":"system","relation":"main_file","file_name":"IST-2016-614-v1+1_s00454-016-9794-2.pdf","checksum":"e0da023abf6b72abd8c6a8c76740d53c","access_level":"open_access","date_created":"2018-12-12T10:10:55Z","content_type":"application/pdf","file_id":"4846"}],"scopus_import":"1","issue":"1","project":[{"name":"Robust Invariants of Nonlinear Systems","call_identifier":"FWF","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","grant_number":"M01980"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"volume":56,"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000377722100005"]},"publist_id":"5799","citation":{"ama":"Franek P, Krcál M. On computability and triviality of well groups. Discrete & Computational Geometry. 2016;56(1):126-164. doi:10.1007/s00454-016-9794-2","ista":"Franek P, Krcál M. 2016. On computability and triviality of well groups. Discrete & Computational Geometry. 56(1), 126–164.","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” Discrete & Computational Geometry, vol. 56, no. 1. Springer, pp. 126–164, 2016.","mla":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry, vol. 56, no. 1, Springer, 2016, pp. 126–64, doi:10.1007/s00454-016-9794-2.","short":"P. Franek, M. Krcál, Discrete & Computational Geometry 56 (2016) 126–164.","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-016-9794-2.","apa":"Franek, P., & Krcál, M. (2016). On computability and triviality of well groups. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9794-2"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","related_material":{"record":[{"id":"1510","status":"public","relation":"earlier_version"}]},"publication":"Discrete & Computational Geometry","has_accepted_license":"1","oa_version":"Published Version","doi":"10.1007/s00454-016-9794-2","oa":1,"publisher":"Springer","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","abstract":[{"text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.","lang":"eng"}],"pubrep_id":"614","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"ddc":["510"],"_id":"1408","title":"On computability and triviality of well groups","day":"01","intvolume":" 56","ec_funded":1,"status":"public","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_published":"2016-07-01T00:00:00Z"},{"pubrep_id":"772","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley-Blackwell","oa":1,"doi":"10.1111/mec.13685","oa_version":"Submitted Version","has_accepted_license":"1","date_published":"2016-06-08T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","intvolume":" 25","day":"08","title":"Genomics of hybridization and its evolutionary consequences","_id":"1409","ddc":["576"],"department":[{"_id":"NiBa"}],"volume":25,"issue":"11","scopus_import":"1","file":[{"file_size":226137,"date_updated":"2020-07-14T12:44:53Z","creator":"system","relation":"main_file","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","checksum":"ede7d0b8a471754f71f17e2b20f3135b","access_level":"open_access","date_created":"2018-12-12T10:10:12Z","file_id":"4797","content_type":"application/pdf"}],"date_created":"2018-12-11T11:51:51Z","author":[{"full_name":"Abbott, Richard","first_name":"Richard","last_name":"Abbott"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"full_name":"Good, Jeffrey","first_name":"Jeffrey","last_name":"Good"}],"file_date_updated":"2020-07-14T12:44:53Z","page":"2325 - 2332","date_updated":"2025-09-18T14:30:06Z","isi":1,"month":"06","publication":"Molecular Ecology","year":"2016","citation":{"mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685.","ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685.","apa":"Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685"},"external_id":{"isi":["000378941100001"]},"publist_id":"5798","publication_status":"published","language":[{"iso":"eng"}]},{"isi":1,"month":"09","date_updated":"2025-09-18T14:29:16Z","page":"10 - 19","file_date_updated":"2020-07-14T12:44:53Z","author":[{"last_name":"Ugalde","first_name":"José","full_name":"Ugalde, José"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"full_name":"Norambuena, Lorena","last_name":"Norambuena","first_name":"Lorena"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Gabriel","last_name":"León","full_name":"León, Gabriel"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"}],"date_created":"2018-12-11T11:51:51Z","file":[{"creator":"dernst","date_updated":"2020-07-14T12:44:53Z","file_size":4338545,"date_created":"2019-04-17T07:41:57Z","content_type":"application/pdf","file_id":"6331","checksum":"ca08de036e6ddc81e6f760e0ccdebd3f","access_level":"open_access","file_name":"2016_PlantScience_Ugalde.pdf","relation":"main_file"}],"scopus_import":"1","volume":250,"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000381545000002"],"pmid":["27457979"]},"publist_id":"5797","citation":{"mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.","ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19.","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19.","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014.","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014"},"year":"2016","publication":"Plant Science","oa_version":"Submitted Version","has_accepted_license":"1","doi":"10.1016/j.plantsci.2016.05.014","oa":1,"publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","pmid":1,"abstract":[{"text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.","lang":"eng"}],"pubrep_id":"1005","acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF.","department":[{"_id":"JiFr"}],"ddc":["581"],"_id":"1410","title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","day":"01","intvolume":" 250","status":"public","article_processing_charge":"No","type":"journal_article","date_published":"2016-09-01T00:00:00Z"},{"language":[{"iso":"eng"}],"publication_status":"published","publist_id":"5796","external_id":{"isi":["000377265600002"],"arxiv":["1302.6475"]},"citation":{"chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1294-9.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics 212 (2016) 37–79.","mla":"Matoušek, Jiří, et al. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics, vol. 212, no. 1, Springer, 2016, pp. 37–79, doi:10.1007/s11856-016-1294-9.","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems of noncrossing curves,” Israel Journal of Mathematics, vol. 212, no. 1. Springer, pp. 37–79, 2016.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 2016;212(1):37-79. doi:10.1007/s11856-016-1294-9","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2016). Untangling two systems of noncrossing curves. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1294-9"},"year":"2016","publication":"Israel Journal of Mathematics","related_material":{"record":[{"status":"public","id":"2244","relation":"earlier_version"}]},"date_updated":"2025-09-18T14:27:54Z","isi":1,"month":"05","page":"37 - 79","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"last_name":"Sedgwick","first_name":"Eric","full_name":"Sedgwick, Eric"},{"full_name":"Tancer, Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"issue":"1","scopus_import":"1","project":[{"name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","_id":"25FA3206-B435-11E9-9278-68D0E5697425","grant_number":"PP00P2_138948"}],"date_created":"2018-12-11T11:51:52Z","volume":212,"acknowledgement":"Supported by the ERC Adv anced Grant No. 267165. ","_id":"1411","department":[{"_id":"UlWa"}],"day":"01","title":"Untangling two systems of noncrossing curves","intvolume":" 212","status":"public","article_processing_charge":"No","date_published":"2016-05-01T00:00:00Z","type":"journal_article","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1302.6475"}],"doi":"10.1007/s11856-016-1294-9","oa":1,"publisher":"Springer","quality_controlled":"1","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn on a compact two-dimensional surface M with boundary. Each αi and each βj is either an arc meeting the boundary of M at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise such that the total number of crossings of the ai with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. The proofs rely, among other things, on a result concerning simultaneous planar drawings of graphs by Erten and Kobourov."}]},{"citation":{"short":"R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242.","chicago":"Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826.","mla":"Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826.","ista":"Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.","ieee":"R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016.","ama":"Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826","apa":"Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826"},"year":"2016","publication":"Computer Graphics Forum","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000377222200022"]},"publist_id":"5795","page":"233 - 242","file_date_updated":"2020-07-14T12:44:53Z","author":[{"first_name":"Ryan","last_name":"Goldade","full_name":"Goldade, Ryan"},{"full_name":"Batty, Christopher","first_name":"Christopher","last_name":"Batty"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"date_created":"2018-12-11T11:51:52Z","issue":"2","file":[{"relation":"main_file","file_name":"IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf","access_level":"open_access","checksum":"8e61387ee2e3bd0e776fbe301629bfd9","file_id":"5000","content_type":"application/pdf","date_created":"2018-12-12T10:13:18Z","file_size":15873858,"date_updated":"2020-07-14T12:44:53Z","creator":"system"}],"scopus_import":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"volume":35,"isi":1,"month":"05","date_updated":"2025-09-18T14:26:23Z","status":"public","article_processing_charge":"No","type":"journal_article","date_published":"2016-05-27T00:00:00Z","acknowledgement":"This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ","department":[{"_id":"ChWo"}],"ddc":["000"],"_id":"1412","title":"A practical method for high-resolution embedded liquid surfaces","day":"27","ec_funded":1,"intvolume":" 35","publisher":"Wiley-Blackwell","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","abstract":[{"lang":"eng","text":"Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods."}],"pubrep_id":"612","has_accepted_license":"1","oa_version":"Submitted Version","doi":"10.1111/cgf.12826","oa":1},{"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","publisher":"Wiley-Blackwell","abstract":[{"text":"This paper generalizes the well-known Diffusion Curves Images (DCI), which are composed of a set of Bezier curves with colors specified on either side. These colors are diffused as Laplace functions over the image domain, which results in smooth color gradients interrupted by the Bezier curves. Our new formulation allows for more color control away from the boundary, providing a similar expressive power as recent Bilaplace image models without introducing associated issues and computational costs. The new model is based on a special Laplace function blending and a new edge blur formulation. We demonstrate that given some user-defined boundary curves over an input raster image, fitting colors and edge blur from the image to the new model and subsequent editing and animation is equally convenient as with DCIs. Numerous examples and comparisons to DCIs are presented.","lang":"eng"}],"doi":"10.1111/cgf.12812","oa_version":"None","article_processing_charge":"No","status":"public","date_published":"2016-05-01T00:00:00Z","type":"journal_article","_id":"1413","department":[{"_id":"ChWo"}],"intvolume":" 35","day":"01","title":"Generalized diffusion curves: An improved vector representation for smooth-shaded images","author":[{"last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Jeschke, Stefan"}],"page":"71 - 79","volume":35,"project":[{"name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23","call_identifier":"FWF","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","issue":"2","date_created":"2018-12-11T11:51:53Z","date_updated":"2025-09-18T14:25:33Z","isi":1,"month":"05","citation":{"apa":"Jeschke, S. (2016). Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12812","chicago":"Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12812.","short":"S. Jeschke, Computer Graphics Forum 35 (2016) 71–79.","mla":"Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 71–79, doi:10.1111/cgf.12812.","ista":"Jeschke S. 2016. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 35(2), 71–79.","ieee":"S. Jeschke, “Generalized diffusion curves: An improved vector representation for smooth-shaded images,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 71–79, 2016.","ama":"Jeschke S. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 2016;35(2):71-79. doi:10.1111/cgf.12812"},"publication":"Computer Graphics Forum","year":"2016","language":[{"iso":"eng"}],"external_id":{"isi":["000377222200008"]},"publist_id":"5794","publication_status":"published"},{"volume":35,"issue":"2","scopus_import":"1","date_created":"2018-12-11T11:51:53Z","author":[{"last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder"},{"full_name":"Miraut, David","last_name":"Miraut","first_name":"David"},{"full_name":"Otaduy, Miguel","last_name":"Otaduy","first_name":"Miguel"}],"page":"385 - 396","date_updated":"2025-09-18T14:24:28Z","month":"05","isi":1,"publication":"Computer Graphics Forum","year":"2016","citation":{"apa":"Miguel Villalba, E., Miraut, D., & Otaduy, M. (2016). Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12840","mla":"Miguel Villalba, Eder, et al. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 385–96, doi:10.1111/cgf.12840.","ieee":"E. Miguel Villalba, D. Miraut, and M. Otaduy, “Modeling and estimation of energy-based hyperelastic objects,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 385–396, 2016.","ista":"Miguel Villalba E, Miraut D, Otaduy M. 2016. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 35(2), 385–396.","ama":"Miguel Villalba E, Miraut D, Otaduy M. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 2016;35(2):385-396. doi:10.1111/cgf.12840","chicago":"Miguel Villalba, Eder, David Miraut, and Miguel Otaduy. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12840.","short":"E. Miguel Villalba, D. Miraut, M. Otaduy, Computer Graphics Forum 35 (2016) 385–396."},"publist_id":"5792","external_id":{"isi":["000377222200036"]},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this paper, we present a method to model hyperelasticity that is well suited for representing the nonlinearity of real-world objects, as well as for estimating it from deformation examples. Previous approaches suffer several limitations, such as lack of integrability of elastic forces, failure to enforce energy convexity, lack of robustness of parameter estimation, or difficulty to model cross-modal effects. Our method avoids these problems by relying on a general energy-based definition of elastic properties. The accuracy of the resulting elastic model is maximized by defining an additive model of separable energy terms, which allow progressive parameter estimation. In addition, our method supports efficient modeling of extreme nonlinearities thanks to energy-limiting constraints. We combine our energy-based model with an optimization method to estimate model parameters from force-deformation examples, and we show successful modeling of diverse deformable objects, including cloth, human finger skin, and internal human anatomy in a medical imaging application."}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley-Blackwell","doi":"10.1111/cgf.12840","oa_version":"None","date_published":"2016-05-01T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","intvolume":" 35","day":"01","title":"Modeling and estimation of energy-based hyperelastic objects","_id":"1414","department":[{"_id":"BeBi"}],"acknowledgement":"This work was funded in part by grants from the Spanish Ministry of Economy (TIN2012-35840), the European Research Council (ERC Starting Grant no. 280135 Animetrics), and the EU FP7 (project no. 601165 WEARHAP)."},{"ddc":["000"],"_id":"1415","department":[{"_id":"ChWo"}],"day":"01","title":"Narrow band FLIP for liquid simulations","intvolume":" 35","status":"public","article_processing_charge":"No","date_published":"2016-05-01T00:00:00Z","type":"journal_article","has_accepted_license":"1","oa_version":"Submitted Version","doi":"10.1111/cgf.12825","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"611","abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation."}],"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000377222200021"]},"publist_id":"5793","citation":{"ieee":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 225–232, 2016.","ista":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 35(2), 225–232.","ama":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825","mla":"Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825.","short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","chicago":"Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825.","apa":"Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016). Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12825"},"year":"2016","publication":"Computer Graphics Forum","date_updated":"2025-09-18T14:25:04Z","month":"05","isi":1,"page":"225 - 232","file_date_updated":"2020-07-14T12:44:53Z","author":[{"last_name":"Ferstl","first_name":"Florian","full_name":"Ferstl, Florian"},{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"last_name":"Westermann","first_name":"Rüdiger","full_name":"Westermann, Rüdiger"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"}],"scopus_import":"1","file":[{"file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf","relation":"main_file","date_created":"2018-12-12T10:12:22Z","content_type":"application/pdf","file_id":"4940","checksum":"984afbe510ed48019025dff1dcc7baad","access_level":"open_access","file_size":5938324,"creator":"system","date_updated":"2020-07-14T12:44:53Z"}],"issue":"2","date_created":"2018-12-11T11:51:53Z","volume":35},{"publication":"Physical Review B - Condensed Matter and Materials Physics","year":"2016","citation":{"ista":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 93(19), 195145.","ama":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 2016;93(19). doi:10.1103/PhysRevB.93.195145","ieee":"E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven Lifshitz transition with dipolar fermions in optical lattices,” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19. American Physical Society, 2016.","mla":"Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:10.1103/PhysRevB.93.195145.","chicago":"Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.195145.","short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016).","apa":"Van Loon, E., Katsnelson, M., Chomaz, L., & Lemeshko, M. (2016). Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.195145"},"publist_id":"5791","external_id":{"arxiv":["1603.09358"],"isi":["000376636900002"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":93,"date_created":"2018-12-11T11:51:54Z","issue":"19","scopus_import":"1","author":[{"full_name":"Van Loon, Erik","last_name":"Van Loon","first_name":"Erik"},{"full_name":"Katsnelson, Mikhail","first_name":"Mikhail","last_name":"Katsnelson"},{"last_name":"Chomaz","first_name":"Lauriane","full_name":"Chomaz, Lauriane"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"isi":1,"month":"05","date_updated":"2025-09-18T14:23:55Z","type":"journal_article","date_published":"2016-05-15T00:00:00Z","article_processing_charge":"No","status":"public","intvolume":" 93","title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices","day":"15","department":[{"_id":"MiLe"}],"_id":"1416","abstract":[{"lang":"eng","text":"Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","arxiv":1,"publisher":"American Physical Society","corr_author":"1","oa":1,"article_number":"195145","doi":"10.1103/PhysRevB.93.195145","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.09358"}],"oa_version":"Preprint"},{"publication":"New Phytologist","year":"2016","citation":{"apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74."},"external_id":{"isi":["000379212800008"]},"publist_id":"5790","publication_status":"published","language":[{"iso":"eng"}],"volume":211,"issue":"1","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:44:53Z","creator":"system","file_size":3828383,"checksum":"23522ced3508ffe7a4f247c4230e6493","access_level":"open_access","date_created":"2018-12-12T10:13:32Z","content_type":"application/pdf","file_id":"5016","relation":"main_file","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf"}],"date_created":"2018-12-11T11:51:54Z","author":[{"full_name":"Simon, Sibu","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"first_name":"Mária","last_name":"Čarná","full_name":"Čarná, Mária"},{"full_name":"Rolčík, Jakub","first_name":"Jakub","last_name":"Rolčík"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"last_name":"Moreno","first_name":"Ignacio","full_name":"Moreno, Ignacio"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"last_name":"Orellana","first_name":"Ariel","full_name":"Orellana, Ariel"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"page":"65 - 74","file_date_updated":"2020-07-14T12:44:53Z","date_updated":"2025-09-18T14:23:21Z","isi":1,"month":"07","date_published":"2016-07-01T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","intvolume":" 211","day":"01","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","_id":"1417","ddc":["581"],"department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","pubrep_id":"1004","abstract":[{"text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.","lang":"eng"}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley-Blackwell","corr_author":"1","oa":1,"doi":"10.1111/nph.14019","has_accepted_license":"1","oa_version":"Submitted Version"},{"_id":"1419","department":[{"_id":"MiLe"}],"day":"29","title":"Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model","ec_funded":1,"intvolume":" 28","status":"public","article_processing_charge":"No","date_published":"2016-03-29T00:00:00Z","type":"journal_article","oa_version":"None","doi":"10.1088/0953-8984/28/17/175701","article_number":"175701","publisher":"IOP Publishing","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We study the superconducting phase of the Hubbard model using the Gutzwiller variational wave function (GWF) and the recently proposed diagrammatic expansion technique (DE-GWF). The DE-GWF method works on the level of the full GWF and in the thermodynamic limit. Here, we consider a finite-size system to study the accuracy of the results as a function of the system size (which is practically unrestricted). We show that the finite-size scaling used, e.g. in the variational Monte Carlo method can lead to significant, uncontrolled errors. The presented research is the first step towards applying the DE-GWF method in studies of inhomogeneous situations, including systems with impurities, defects, inhomogeneous phases, or disorder."}],"language":[{"iso":"eng"}],"publication_status":"published","publist_id":"5788","external_id":{"isi":["000374393100011"]},"citation":{"apa":"Tomski, A., & Kaczmarczyk, J. (2016). Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/0953-8984/28/17/175701","mla":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter, vol. 28, no. 17, 175701, IOP Publishing, 2016, doi:10.1088/0953-8984/28/17/175701.","ieee":"A. Tomski and J. Kaczmarczyk, “Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model,” Journal of Physics: Condensed Matter, vol. 28, no. 17. IOP Publishing, 2016.","ama":"Tomski A, Kaczmarczyk J. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 2016;28(17). doi:10.1088/0953-8984/28/17/175701","ista":"Tomski A, Kaczmarczyk J. 2016. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 28(17), 175701.","chicago":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter. IOP Publishing, 2016. https://doi.org/10.1088/0953-8984/28/17/175701.","short":"A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016)."},"year":"2016","publication":"Journal of Physics: Condensed Matter","date_updated":"2025-09-18T14:22:40Z","isi":1,"month":"03","author":[{"full_name":"Tomski, Andrzej","first_name":"Andrzej","last_name":"Tomski"},{"full_name":"Kaczmarczyk, Jan","last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"issue":"17","scopus_import":"1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:51:55Z","volume":28},{"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarína","last_name":"Bod'ová","full_name":"Bod'ová, Katarína"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"page":"1523 - 1548","volume":202,"date_created":"2018-12-11T11:51:55Z","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"scopus_import":"1","issue":"4","month":"04","isi":1,"date_updated":"2025-09-18T14:22:05Z","citation":{"apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016."},"publication":"Genetics","year":"2016","language":[{"iso":"eng"}],"external_id":{"arxiv":["1510.08344"],"isi":["000373959100022"]},"publist_id":"5787","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","arxiv":1,"publisher":"Genetics Society of America","corr_author":"1","abstract":[{"text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ","lang":"eng"}],"doi":"10.1534/genetics.115.184127","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"oa_version":"Preprint","oa":1,"article_processing_charge":"No","status":"public","type":"journal_article","date_published":"2016-04-06T00:00:00Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"_id":"1420","intvolume":" 202","ec_funded":1,"title":"A general approximation for the dynamics of quantitative traits","day":"06"},{"status":"public","article_processing_charge":"No","citation":{"apa":"Bak, S., Bogomolov, S., Henzinger, T. A., Johnson, T., & Prakash, P. (2016). Scalable static hybridization methods for analysis of nonlinear systems (pp. 155–164). Presented at the HSCC: Hybrid Systems - Computation and Control, Vienna, Austria: Springer. https://doi.org/10.1145/2883817.2883837","chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, Taylor Johnson, and Pradyot Prakash. “Scalable Static Hybridization Methods for Analysis of Nonlinear Systems,” 155–64. Springer, 2016. https://doi.org/10.1145/2883817.2883837.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","ista":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. 2016. Scalable static hybridization methods for analysis of nonlinear systems. HSCC: Hybrid Systems - Computation and Control, 155–164.","ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, T. Johnson, and P. Prakash, “Scalable static hybridization methods for analysis of nonlinear systems,” presented at the HSCC: Hybrid Systems - Computation and Control, Vienna, Austria, 2016, pp. 155–164.","ama":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. Scalable static hybridization methods for analysis of nonlinear systems. In: Springer; 2016:155-164. doi:10.1145/2883817.2883837","mla":"Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837."},"year":"2016","type":"conference","date_published":"2016-04-11T00:00:00Z","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"_id":"1421","title":"Scalable static hybridization methods for analysis of nonlinear systems","publication_status":"published","day":"11","external_id":{"isi":["000390844400018"]},"publist_id":"5786","ec_funded":1,"publisher":"Springer","page":"155 - 164","author":[{"last_name":"Bak","first_name":"Stanley","full_name":"Bak, Stanley"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Johnson, Taylor","first_name":"Taylor","last_name":"Johnson"},{"last_name":"Prakash","first_name":"Pradyot","full_name":"Prakash, Pradyot"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","date_created":"2018-12-11T11:51:55Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Hybridization methods enable the analysis of hybrid automata with complex, nonlinear dynamics through a sound abstraction process. Complex dynamics are converted to simpler ones with added noise, and then analysis is done using a reachability method for the simpler dynamics. Several such recent approaches advocate that only "dynamic" hybridization techniquesi.e., those where the dynamics are abstracted on-The-fly during a reachability computation are effective. In this paper, we demonstrate this is not the case, and create static hybridization methods that are more scalable than earlier approaches. The main insight in our approach is that quick, numeric simulations can be used to guide the process, eliminating the need for an exponential number of hybridization domains. Transitions between domains are generally timetriggered, avoiding accumulated error from geometric intersections. We enhance our static technique by combining time-Triggered transitions with occasional space-Triggered transitions, and demonstrate the benefits of the combined approach in what we call mixed-Triggered hybridization. Finally, error modes are inserted to confirm that the reachable states stay within the hybridized regions. The developed techniques can scale to higher dimensions than previous static approaches, while enabling the parallelization of the main performance bottleneck for many dynamic hybridization approaches: The nonlinear optimization required for sound dynamics abstraction. We implement our method as a model transformation pass in the HYST tool, and perform reachability analysis and evaluation using an unmodified version of SpaceEx on nonlinear models with up to six dimensions."}],"oa_version":"None","doi":"10.1145/2883817.2883837","conference":{"location":"Vienna, Austria","end_date":"2016-04-14","start_date":"2016-04-12","name":"HSCC: Hybrid Systems - Computation and Control"},"isi":1,"month":"04","date_updated":"2025-09-18T14:21:28Z"},{"language":[{"iso":"eng"}],"publist_id":"5785","external_id":{"isi":["000378844700002"]},"publication_status":"published","citation":{"apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923.","ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5"},"publication":"Letters in Mathematical Physics","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2016","month":"07","isi":1,"date_updated":"2025-09-18T14:20:53Z","author":[{"full_name":"Frank, Rupert","first_name":"Rupert","last_name":"Frank"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"file_date_updated":"2020-07-14T12:44:53Z","page":"913 - 923","volume":106,"date_created":"2018-12-11T11:51:56Z","file":[{"date_updated":"2020-07-14T12:44:53Z","creator":"system","file_size":458968,"checksum":"fb404923d8ca9a1faeb949561f26cbea","access_level":"open_access","date_created":"2018-12-12T10:15:57Z","content_type":"application/pdf","file_id":"5181","relation":"main_file","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf"}],"issue":"7","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"scopus_import":"1","department":[{"_id":"RoSe"}],"_id":"1422","ddc":["510","530"],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","intvolume":" 106","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","day":"01","article_processing_charge":"Yes (via OA deal)","status":"public","type":"journal_article","date_published":"2016-07-01T00:00:00Z","doi":"10.1007/s11005-016-0847-5","oa_version":"Published Version","has_accepted_license":"1","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publisher":"Springer","corr_author":"1","abstract":[{"lang":"eng","text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior."}],"pubrep_id":"591"},{"publication_status":"published","publist_id":"5784","external_id":{"isi":["000375448500002"]},"language":[{"iso":"eng"}],"year":"2016","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Scientific Reports","citation":{"apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676."},"month":"05","isi":1,"date_updated":"2025-09-18T14:15:33Z","date_created":"2018-12-11T11:51:56Z","scopus_import":"1","file":[{"access_level":"open_access","checksum":"ee17c482370d2e1b3add393710d3c696","file_id":"5327","content_type":"application/pdf","date_created":"2018-12-12T10:18:08Z","relation":"main_file","file_name":"IST-2016-590-v1+1_srep25676.pdf","date_updated":"2020-07-14T12:44:53Z","creator":"system","file_size":1349915}],"volume":6,"file_date_updated":"2020-07-14T12:44:53Z","author":[{"last_name":"Baek","first_name":"Seung","full_name":"Baek, Seung"},{"full_name":"Jeong, Hyeongchai","first_name":"Hyeongchai","last_name":"Jeong"},{"full_name":"Hilbe, Christian","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"title":"Comparing reactive and memory-one strategies of direct reciprocity","day":"10","intvolume":" 6","acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","department":[{"_id":"KrCh"}],"_id":"1423","ddc":["000"],"type":"journal_article","date_published":"2016-05-10T00:00:00Z","status":"public","article_processing_charge":"No","article_number":"25676","oa":1,"oa_version":"Published Version","has_accepted_license":"1","doi":"10.1038/srep25676","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation."}],"pubrep_id":"590","corr_author":"1","publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1"}]