[{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10933"}],"intvolume":"        98","citation":{"chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>.","ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134.","apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., &#38; Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>.","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. 2018;98(15). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>","ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” <i>Physical Review B</i>, vol. 98, no. 15. American Physical Society, 2018."},"doi":"10.1103/PhysRevB.98.155134","publication_status":"published","oa_version":"Preprint","date_published":"2018-10-22T00:00:00Z","status":"public","oa":1,"month":"10","abstract":[{"text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization.","lang":"eng"}],"arxiv":1,"issue":"15","date_updated":"2023-10-10T13:28:49Z","year":"2018","acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"155134","_id":"44","article_processing_charge":"No","publist_id":"8010","volume":98,"quality_controlled":"1","external_id":{"arxiv":["1806.10933"],"isi":["000447919100001"]},"publication":"Physical Review B","date_created":"2018-12-11T11:44:19Z","type":"journal_article","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","day":"22","isi":1,"author":[{"first_name":"C J","last_name":"Turner","full_name":"Turner, C J"},{"last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","first_name":"Alexios","full_name":"Michailidis, Alexios"},{"last_name":"Abanin","first_name":"D A","full_name":"Abanin, D A"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"full_name":"Papić, Z","first_name":"Z","last_name":"Papić"}]},{"title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Bio-protocol","file":[{"access_level":"open_access","checksum":"6644ba698206eda32b0abf09128e63e3","creator":"system","file_id":"5299","date_created":"2018-12-12T10:17:43Z","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","date_updated":"2020-07-14T12:46:29Z","file_size":11352389,"relation":"main_file","content_type":"application/pdf"}],"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin","full_name":"Li, Lanxin"},{"full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","orcid":"0000-0002-9767-8699","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"day":"05","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","related_material":{"record":[{"id":"10083","relation":"dissertation_contains","status":"public"}]},"quality_controlled":"1","volume":8,"article_type":"original","pubrep_id":"970","article_processing_charge":"No","publist_id":"7381","department":[{"_id":"JiFr"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Bio-protocol","date_created":"2018-12-11T11:46:30Z","has_accepted_license":"1","ec_funded":1,"month":"01","oa":1,"publication_identifier":{"eissn":["2331-8325"]},"status":"public","_id":"442","year":"2018","issue":"1","abstract":[{"lang":"eng","text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH."}],"date_updated":"2024-10-29T10:22:43Z","intvolume":"         8","citation":{"short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. <i>Bio-protocol</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.21769/BioProtoc.2685\">10.21769/BioProtoc.2685</a>","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” <i>Bio-protocol</i>, vol. 8, no. 1. Bio-protocol, 2018.","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” <i>Bio-Protocol</i>, vol. 8, no. 1, Bio-protocol, 2018, doi:<a href=\"https://doi.org/10.21769/BioProtoc.2685\">10.21769/BioProtoc.2685</a>.","apa":"Li, L., Krens, G., Fendrych, M., &#38; Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. <i>Bio-Protocol</i>. Bio-protocol. <a href=\"https://doi.org/10.21769/BioProtoc.2685\">https://doi.org/10.21769/BioProtoc.2685</a>","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” <i>Bio-Protocol</i>. Bio-protocol, 2018. <a href=\"https://doi.org/10.21769/BioProtoc.2685\">https://doi.org/10.21769/BioProtoc.2685</a>."},"ddc":["576","581"],"file_date_updated":"2020-07-14T12:46:29Z","date_published":"2018-01-05T00:00:00Z","oa_version":"Published Version","doi":"10.21769/BioProtoc.2685","publication_status":"published"},{"_id":"446","issue":"3","arxiv":1,"abstract":[{"lang":"eng","text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z &gt; 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential."}],"date_updated":"2023-09-19T10:09:40Z","year":"2018","month":"03","status":"public","oa":1,"oa_version":"Preprint","date_published":"2018-03-01T00:00:00Z","doi":"10.1002/cpa.21717","publication_status":"published","intvolume":"        71","citation":{"mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” <i>Communications on Pure and Applied Mathematics</i>, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:<a href=\"https://doi.org/10.1002/cpa.21717\">10.1002/cpa.21717</a>.","ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","apa":"Frank, R., Nam, P., &#38; Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cpa.21717\">https://doi.org/10.1002/cpa.21717</a>","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” <i>Communications on Pure and Applied Mathematics</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1002/cpa.21717\">https://doi.org/10.1002/cpa.21717</a>.","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. <i>Communications on Pure and Applied Mathematics</i>. 2018;71(3):577-614. doi:<a href=\"https://doi.org/10.1002/cpa.21717\">10.1002/cpa.21717</a>","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” <i>Communications on Pure and Applied Mathematics</i>, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614."},"main_file_link":[{"url":"https://arxiv.org/abs/1606.07355","open_access":"1"}],"isi":1,"author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Phan Thanh","first_name":"Nam","full_name":"Phan Thanh, Nam"},{"full_name":"Van Den Bosch, Hanne","first_name":"Hanne","last_name":"Van Den Bosch"}],"acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley-Blackwell","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","type":"journal_article","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"publication":"Communications on Pure and Applied Mathematics","page":"577 - 614","date_created":"2018-12-11T11:46:31Z","quality_controlled":"1","volume":71,"external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"article_type":"original","article_processing_charge":"No","publist_id":"7377"},{"oa":1,"status":"public","month":"02","year":"2018","date_updated":"2023-09-11T14:10:57Z","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"issue":"3","_id":"448","ddc":["576"],"file_date_updated":"2020-07-14T12:46:30Z","scopus_import":"1","citation":{"apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>.","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ieee":"M. Harrison <i>et al.</i>, “Hemimetabolous genomes reveal molecular basis of termite eusociality,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. 2018;2(3):557-566. doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>"},"intvolume":"         2","publication_status":"published","doi":"10.1038/s41559-017-0459-1","date_published":"2018-02-05T00:00:00Z","oa_version":"Published Version","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","publisher":"Springer Nature","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"05","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","file":[{"file_size":3730583,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"874953136ac125e65f37971d3cabc5b7","creator":"system","file_id":"4731","date_created":"2018-12-12T10:09:08Z","file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","date_updated":"2020-07-14T12:46:30Z"}],"author":[{"last_name":"Harrison","first_name":"Mark","full_name":"Harrison, Mark"},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"full_name":"Robertson, Hugh","first_name":"Hugh","last_name":"Robertson"},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"first_name":"Tristan","last_name":"Bitard Feildel","full_name":"Bitard Feildel, Tristan"},{"first_name":"Hsu","last_name":"Chao","full_name":"Chao, Hsu"},{"full_name":"Childers, Christopher","first_name":"Christopher","last_name":"Childers"},{"full_name":"Dinh, Huyen","last_name":"Dinh","first_name":"Huyen"},{"last_name":"Doddapaneni","first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"full_name":"Gowin, Johannes","first_name":"Johannes","last_name":"Gowin"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"last_name":"Han","first_name":"Yi","full_name":"Han, Yi"},{"last_name":"Hu","first_name":"Haofu","full_name":"Hu, Haofu"},{"first_name":"Daniel","last_name":"Hughes","full_name":"Hughes, Daniel"},{"full_name":"Huylmans, Ann K","first_name":"Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kemena, Karsten","first_name":"Karsten","last_name":"Kemena"},{"last_name":"Kremer","first_name":"Lukas","full_name":"Kremer, Lukas"},{"full_name":"Lee, Sandra","first_name":"Sandra","last_name":"Lee"},{"last_name":"López Ezquerra","first_name":"Alberto","full_name":"López Ezquerra, Alberto"},{"full_name":"Mallet, Ludovic","last_name":"Mallet","first_name":"Ludovic"},{"full_name":"Monroy Kuhn, Jose","last_name":"Monroy Kuhn","first_name":"Jose"},{"last_name":"Moser","first_name":"Annabell","full_name":"Moser, Annabell"},{"first_name":"Shwetha","last_name":"Murali","full_name":"Murali, Shwetha"},{"first_name":"Donna","last_name":"Muzny","full_name":"Muzny, Donna"},{"last_name":"Otani","first_name":"Saria","full_name":"Otani, Saria"},{"first_name":"Maria","last_name":"Piulachs","full_name":"Piulachs, Maria"},{"last_name":"Poelchau","first_name":"Monica","full_name":"Poelchau, Monica"},{"full_name":"Qu, Jiaxin","last_name":"Qu","first_name":"Jiaxin"},{"full_name":"Schaub, Florentine","first_name":"Florentine","last_name":"Schaub"},{"first_name":"Ayako","last_name":"Wada Katsumata","full_name":"Wada Katsumata, Ayako"},{"full_name":"Worley, Kim","last_name":"Worley","first_name":"Kim"},{"first_name":"Qiaolin","last_name":"Xie","full_name":"Xie, Qiaolin"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"first_name":"Michael","last_name":"Poulsen","full_name":"Poulsen, Michael"},{"first_name":"Richard","last_name":"Gibbs","full_name":"Gibbs, Richard"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"full_name":"Belles, Xavier","first_name":"Xavier","last_name":"Belles"},{"first_name":"Judith","last_name":"Korb","full_name":"Korb, Judith"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"}],"isi":1,"publist_id":"7375","pubrep_id":"969","article_processing_charge":"No","related_material":{"record":[{"relation":"research_data","status":"public","id":"9841"}]},"external_id":{"isi":["000426559600026"]},"quality_controlled":"1","volume":2,"page":"557-566","date_created":"2018-12-11T11:46:32Z","publication":"Nature Ecology and Evolution","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"type":"journal_article"},{"ddc":["581"],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:30Z","intvolume":"        14","citation":{"short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. <i>PLoS Genetics</i>. 2018;14(1). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007177\">10.1371/journal.pgen.1007177</a>","ieee":"T. Prat <i>et al.</i>, “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” <i>PLoS Genetics</i>, vol. 14, no. 1. Public Library of Science, 2018.","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1).","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” <i>PLoS Genetics</i>, vol. 14, no. 1, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007177\">10.1371/journal.pgen.1007177</a>.","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007177\">https://doi.org/10.1371/journal.pgen.1007177</a>","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” <i>PLoS Genetics</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pgen.1007177\">https://doi.org/10.1371/journal.pgen.1007177</a>."},"publication_status":"published","doi":"10.1371/journal.pgen.1007177","date_published":"2018-01-29T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","ec_funded":1,"month":"01","year":"2018","date_updated":"2025-05-07T11:12:28Z","issue":"1","abstract":[{"text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development.","lang":"eng"}],"_id":"449","publist_id":"7373","pubrep_id":"967","article_processing_charge":"Yes","related_material":{"record":[{"id":"1127","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"7172"},{"relation":"dissertation_contains","status":"public","id":"8822"}]},"external_id":{"isi":["000423718600034"]},"volume":14,"quality_controlled":"1","date_created":"2018-12-11T11:46:32Z","publication":"PLoS Genetics","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"type":"journal_article","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","publisher":"Public Library of Science","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"29","file":[{"file_size":24709062,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"system","file_id":"4843","checksum":"0276d66788ec076f4924164a39e6a712","date_created":"2018-12-12T10:10:52Z","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","date_updated":"2020-07-14T12:46:30Z"}],"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"isi":1,"author":[{"last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Prat, Tomas"},{"orcid":"0000-0003-2140-7195","first_name":"Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","full_name":"Hajny, Jakub"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K","full_name":"Vasileva, Mina K"},{"first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"first_name":"Markus","last_name":"Schmid","full_name":"Schmid, Markus"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí"}]},{"external_id":{"isi":["000424318200001"]},"quality_controlled":"1","volume":9,"publist_id":"7368","article_processing_charge":"No","pubrep_id":"964","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"type":"journal_article","date_created":"2018-12-11T11:46:34Z","publication":"Nature Communications","has_accepted_license":"1","title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":843646,"content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:09:18Z","date_updated":"2020-07-14T12:46:31Z","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","access_level":"open_access","creator":"system","file_id":"4741","checksum":"b6b90367545b4c615891c960ab0567f1"}],"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"isi":1,"author":[{"orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes"},{"full_name":"Hilbe, Christian","first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rand, David","last_name":"Rand","first_name":"David"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"day":"07","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","intvolume":"         9","citation":{"apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., &#38; Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-02721-8\">https://doi.org/10.1038/s41467-017-02721-8</a>","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” <i>Nature Communications</i>, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-017-02721-8\">10.1038/s41467-017-02721-8</a>.","chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-017-02721-8\">https://doi.org/10.1038/s41467-017-02721-8</a>.","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018.","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-02721-8\">10.1038/s41467-017-02721-8</a>","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018)."},"ddc":["004"],"file_date_updated":"2020-07-14T12:46:31Z","scopus_import":"1","date_published":"2018-02-07T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41467-017-02721-8","ec_funded":1,"month":"02","oa":1,"status":"public","_id":"454","article_number":"555","year":"2018","date_updated":"2023-09-11T12:51:03Z","abstract":[{"text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.","lang":"eng"}],"issue":"1"},{"ddc":["510","539"],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:31Z","citation":{"chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” <i>Annales Henri Poincare</i>. Birkhäuser, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0644-z\">https://doi.org/10.1007/s00023-018-0644-z</a>.","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","apa":"Benedikter, N. P., Sok, J., &#38; Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. <i>Annales Henri Poincare</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00023-018-0644-z\">https://doi.org/10.1007/s00023-018-0644-z</a>","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” <i>Annales Henri Poincare</i>, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:<a href=\"https://doi.org/10.1007/s00023-018-0644-z\">10.1007/s00023-018-0644-z</a>.","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” <i>Annales Henri Poincare</i>, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. <i>Annales Henri Poincare</i>. 2018;19(4):1167-1214. doi:<a href=\"https://doi.org/10.1007/s00023-018-0644-z\">10.1007/s00023-018-0644-z</a>"},"intvolume":"        19","publication_status":"published","doi":"10.1007/s00023-018-0644-z","date_published":"2018-04-01T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","month":"04","year":"2018","date_updated":"2023-09-19T10:07:41Z","abstract":[{"lang":"eng","text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities"}],"issue":"4","_id":"455","publist_id":"7367","article_processing_charge":"No","pubrep_id":"993","external_id":{"isi":["000427578900006"]},"volume":19,"quality_controlled":"1","date_created":"2018-12-11T11:46:34Z","page":"1167 - 1214","publication":"Annales Henri Poincare","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"type":"journal_article","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","publisher":"Birkhäuser","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["Annales Henri Poincare"],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","file":[{"file_size":923252,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"883eeccba8384ad7fcaa28761d99a0fa","file_id":"4914","creator":"system","date_created":"2018-12-12T10:11:57Z","date_updated":"2020-07-14T12:46:31Z","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf"}],"author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","first_name":"Niels P","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P"},{"first_name":"Jérémy","last_name":"Sok","full_name":"Sok, Jérémy"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}],"isi":1},{"ddc":["510"],"file_date_updated":"2020-07-14T12:45:45Z","intvolume":"        75","citation":{"ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in <i>Proceedings of the 31st Conference On Learning Theory</i>, 2017, vol. 75, pp. 228–249.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: <i>Proceedings of the 31st Conference On Learning Theory</i>. Vol 75. ML Research Press; 2017:228-249.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249.","chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In <i>Proceedings of the 31st Conference On Learning Theory</i>, 75:228–49. ML Research Press, 2017.","ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory  vol. 75, 228–249.","apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In <i>Proceedings of the 31st Conference On Learning Theory</i> (Vol. 75, pp. 228–249). ML Research Press.","mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” <i>Proceedings of the 31st Conference On Learning Theory</i>, vol. 75, ML Research Press, 2017, pp. 228–49."},"publication_status":"published","conference":{"end_date":"2018-07-09","start_date":"2018-07-06","name":"COLT: Annual Conference on Learning Theory "},"date_published":"2017-12-27T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","ec_funded":1,"month":"12","year":"2017","date_updated":"2023-10-17T12:32:13Z","abstract":[{"text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation.","lang":"eng"}],"arxiv":1,"_id":"274","publist_id":"7628","article_processing_charge":"No","external_id":{"arxiv":["1608.04223"]},"quality_controlled":"1","volume":75,"page":"228-249","date_created":"2018-12-11T11:45:33Z","publication":"Proceedings of the 31st Conference On Learning Theory","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"type":"conference","title":"A faster approximation algorithm for the Gibbs partition function","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"27","file":[{"content_type":"application/pdf","relation":"main_file","file_size":408974,"date_updated":"2020-07-14T12:45:45Z","file_name":"2018_PMLR_Kolmogorov.pdf","date_created":"2020-05-12T09:23:27Z","file_id":"7820","checksum":"89db06a0e8083524449cb59b56bf4e5b","creator":"dernst","access_level":"open_access"}],"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}]},{"has_accepted_license":"1","date_created":"2018-12-11T11:45:46Z","type":"conference","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"publist_id":"7552","volume":999,"quality_controlled":"1","external_id":{"arxiv":["1611.03701"]},"related_material":{"record":[{"status":"public","relation":"later_version","id":"6013"}]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"14","author":[{"full_name":"Camus, Nicolas","first_name":"Nicolas","last_name":"Camus"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp"},{"last_name":"Fechner","first_name":"Lutz","full_name":"Fechner, Lutz"},{"full_name":"Klaiber, Michael","last_name":"Klaiber","first_name":"Michael"},{"full_name":"Laux, Martin","last_name":"Laux","first_name":"Martin"},{"first_name":"Yonghao","last_name":"Mi","full_name":"Mi, Yonghao"},{"full_name":"Hatsagortsyan, Karen","first_name":"Karen","last_name":"Hatsagortsyan"},{"full_name":"Pfeifer, Thomas","first_name":"Thomas","last_name":"Pfeifer"},{"first_name":"Cristoph","last_name":"Keitel","full_name":"Keitel, Cristoph"},{"first_name":"Robert","last_name":"Moshammer","full_name":"Moshammer, Robert"}],"file":[{"file_size":949321,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","file_id":"5871","creator":"dernst","date_created":"2019-01-22T08:34:10Z","date_updated":"2020-07-14T12:46:00Z","file_name":"2017_Physics_Camus.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","title":"Experimental evidence for Wigner's tunneling time","alternative_title":["Journal of Physics: Conference Series"],"doi":"10.1088/1742-6596/999/1/012004","conference":{"name":"Annual International Laser Physics Workshop LPHYS","start_date":"2017-08-17","location":"Kazan, Russian Federation","end_date":"2017-08-21"},"publication_status":"published","oa_version":"Published Version","date_published":"2017-07-14T00:00:00Z","file_date_updated":"2020-07-14T12:46:00Z","scopus_import":1,"ddc":["530"],"citation":{"chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>.","mla":"Camus, Nicolas, et al. <i>Experimental Evidence for Wigner’s Tunneling Time</i>. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>","ieee":"N. Camus <i>et al.</i>, “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017."},"intvolume":"       999","arxiv":1,"abstract":[{"text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.","lang":"eng"}],"issue":"1","date_updated":"2023-02-23T12:36:07Z","year":"2017","article_number":"012004","_id":"313","status":"public","publication_identifier":{"issn":["17426588"]},"oa":1,"month":"07"},{"date_published":"2017-06-01T00:00:00Z","oa_version":"None","publication_status":"published","doi":"10.1016/j.ic.2016.10.006","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” <i>Information and Computation</i>, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. <i>Information and Computation</i>. 2017;254(2):143-166. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2017). Quantitative fair simulation games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>."},"intvolume":"       254","scopus_import":"1","_id":"1066","year":"2017","date_updated":"2023-09-20T12:07:48Z","issue":"2","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"ec_funded":1,"month":"06","status":"public","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"type":"journal_article","page":"143 - 166","date_created":"2018-12-11T11:49:58Z","publication":"Information and Computation","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5428"}]},"external_id":{"isi":["000402025600002"]},"quality_controlled":"1","volume":254,"publist_id":"6322","article_processing_charge":"No","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"isi":1,"day":"01","title":"Quantitative fair simulation games","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"27","file":[{"content_type":"application/pdf","relation":"main_file","file_size":6866187,"date_updated":"2018-12-12T10:10:57Z","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_created":"2018-12-12T10:10:57Z","creator":"system","file_id":"4849","access_level":"open_access"}],"author":[{"first_name":"Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Bock, Martin","first_name":"Martin","last_name":"Bock"},{"full_name":"Krens, Gabriel","first_name":"Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"isi":1,"project":[{"_id":"2524F500-B435-11E9-9278-68D0E5697425","grant_number":"201439","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Cell Press","publication":"Developmental Cell","page":"354 - 366","date_created":"2018-12-11T11:49:58Z","has_accepted_license":"1","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","pubrep_id":"869","publist_id":"6320","quality_controlled":"1","volume":40,"external_id":{"isi":["000395368300007"]},"year":"2017","abstract":[{"lang":"eng","text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction."}],"issue":"4","date_updated":"2023-09-20T12:06:27Z","_id":"1067","acknowledged_ssus":[{"_id":"PreCl"}],"oa":1,"publication_identifier":{"issn":["15345807"]},"status":"public","ec_funded":1,"month":"02","doi":"10.1016/j.devcel.2017.01.010","publication_status":"published","date_published":"2017-02-27T00:00:00Z","oa_version":"Published Version","ddc":["572","597"],"file_date_updated":"2018-12-12T10:10:57Z","scopus_import":"1","intvolume":"        40","citation":{"short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. 2017;40(4):354-366. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” <i>Developmental Cell</i>, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., &#38; Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>."}},{"acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","day":"01","isi":1,"author":[{"first_name":"Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"}],"project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Mathematical Society","title":"The Morse theory of Čech and delaunay complexes","publication":"Transactions of the American Mathematical Society","date_created":"2018-12-11T11:49:59Z","page":"3741 - 3762","type":"journal_article","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","article_type":"original","publist_id":"6311","quality_controlled":"1","volume":369,"external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"arxiv":1,"abstract":[{"text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field.","lang":"eng"}],"issue":"5","date_updated":"2023-09-20T12:05:56Z","year":"2017","_id":"1072","status":"public","oa":1,"month":"05","ec_funded":1,"doi":"10.1090/tran/6991","publication_status":"published","oa_version":"Preprint","date_published":"2017-05-01T00:00:00Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"intvolume":"       369","citation":{"chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","apa":"Bauer, U., &#38; Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>"}},{"status":"public","publication_identifier":{"issn":["01795376"]},"oa":1,"month":"06","date_updated":"2023-09-20T12:01:28Z","issue":"4","abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"year":"2017","_id":"1073","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"scopus_import":"1","intvolume":"        54","citation":{"apa":"Čadek, M., Krcál, M., &#38; Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>"},"publication_status":"published","doi":"10.1007/s00454-016-9855-6","oa_version":"Submitted Version","date_published":"2017-06-01T00:00:00Z","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Algorithmic solvability of the lifting extension problem","day":"01","isi":1,"author":[{"full_name":"Čadek, Martin","first_name":"Martin","last_name":"Čadek"},{"last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","full_name":"Krcál, Marek"},{"last_name":"Vokřínek","first_name":"Lukáš","full_name":"Vokřínek, Lukáš"}],"publist_id":"6309","article_processing_charge":"No","external_id":{"isi":["000400072700008"]},"volume":54,"quality_controlled":"1","page":"915 - 965","date_created":"2018-12-11T11:50:00Z","publication":"Discrete & Computational Geometry","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}]},{"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Genetics Society of America","day":"01","author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald"},{"last_name":"Coop","first_name":"Graham","full_name":"Coop, Graham"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"isi":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"article_processing_charge":"No","publist_id":"6307","related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"volume":205,"quality_controlled":"1","external_id":{"isi":["000395807200023"]},"publication":"Genetics","date_created":"2018-12-11T11:50:00Z","page":"1335 - 1351","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"type":"journal_article","publication_identifier":{"issn":["00166731"]},"oa":1,"status":"public","ec_funded":1,"month":"03","year":"2017","issue":"3","abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"date_updated":"2025-05-28T11:42:51Z","_id":"1074","main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"scopus_import":"1","intvolume":"       205","citation":{"ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” <i>Genetics</i>, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>.","apa":"Ringbauer, H., Coop, G., &#38; Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>."},"doi":"10.1534/genetics.116.196220","publication_status":"published","date_published":"2017-03-01T00:00:00Z","oa_version":"Preprint"},{"year":"2017","date_updated":"2023-09-20T11:57:23Z","abstract":[{"lang":"eng","text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed."}],"issue":"2","_id":"1076","article_number":"023403","publication_identifier":{"issn":["24699926"]},"oa":1,"status":"public","ec_funded":1,"month":"02","publication_status":"published","doi":"10.1103/PhysRevA.95.023403","date_published":"2017-02-01T00:00:00Z","oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"citation":{"chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>.","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation.  Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., &#38; Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2. American Physical Society, 2017.","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel,  Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017)."},"intvolume":"        95","day":"01","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"author":[{"last_name":"Klaiber","first_name":"Michael","full_name":"Klaiber, Michael"},{"first_name":"Jiří","last_name":"Daněk","full_name":"Daněk, Jiří"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp","orcid":"0000-0001-5973-0874"},{"full_name":"Hatsagortsyan, Karen","first_name":"Karen","last_name":"Hatsagortsyan"},{"full_name":"Keitel, Christoph","last_name":"Keitel","first_name":"Christoph"}],"isi":1,"title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:50:01Z","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"type":"journal_article","publist_id":"6305","article_processing_charge":"No","external_id":{"isi":["000400571700011"]},"quality_controlled":"1","volume":95},{"status":"public","publication_identifier":{"issn":["17425689"]},"oa":1,"month":"01","ec_funded":1,"date_updated":"2025-05-28T11:42:51Z","issue":"126","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"year":"2017","article_number":"20160139","_id":"1077","scopus_import":"1","file_date_updated":"2019-01-18T09:14:02Z","ddc":["570"],"intvolume":"        14","citation":{"short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139."},"publication_status":"published","doi":"10.1098/rsif.2016.0139","oa_version":"Published Version","date_published":"2017-01-04T00:00:00Z","publisher":"Royal Society of London","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"04","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"isi":1,"author":[{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vladar, Harold","first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"file":[{"access_level":"open_access","file_id":"5843","creator":"dernst","date_created":"2019-01-18T09:14:02Z","date_updated":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","file_size":1092015,"success":1,"content_type":"application/pdf","relation":"main_file"}],"publist_id":"6303","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000393380400001"]},"quality_controlled":"1","volume":14,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9864"}]},"has_accepted_license":"1","date_created":"2018-12-11T11:50:01Z","publication":"Journal of the Royal Society Interface","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}]},{"isi":1,"author":[{"orcid":"0000-0002-6862-1247","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel"},{"full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"file":[{"file_size":57678,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5219","creator":"system","date_created":"2018-12-12T10:16:31Z","date_updated":"2018-12-12T10:16:31Z","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf"},{"access_level":"open_access","file_id":"5220","creator":"system","date_created":"2018-12-12T10:16:32Z","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","date_updated":"2018-12-12T10:16:32Z","file_size":1317820,"relation":"main_file","content_type":"application/pdf"}],"day":"18","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Journal of Visualized Experiments","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","type":"journal_article","department":[{"_id":"JiFr"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Journal of visualized experiments JoVE","date_created":"2018-12-11T11:50:01Z","volume":2017,"external_id":{"isi":["000397847200041"]},"related_material":{"record":[{"id":"5565","relation":"popular_science","status":"public"}]},"pubrep_id":"808","article_processing_charge":"No","publist_id":"6302","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"article_number":"e55044","_id":"1078","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. "}],"issue":"119","date_updated":"2025-05-07T11:12:33Z","year":"2017","month":"01","ec_funded":1,"status":"public","oa":1,"oa_version":"Published Version","date_published":"2017-01-18T00:00:00Z","doi":"10.3791/55044","publication_status":"published","intvolume":"      2017","citation":{"chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017)."},"file_date_updated":"2018-12-12T10:16:32Z","scopus_import":"1","ddc":["580"]},{"doi":"10.1007/s11040-017-9238-0","publication_status":"published","date_published":"2017-06-01T00:00:00Z","oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"intvolume":"        20","citation":{"mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2, 6, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>.","apa":"Nam, P., &#38; Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6.","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017.","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017)."},"year":"2017","issue":"2","abstract":[{"lang":"eng","text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers."}],"date_updated":"2023-09-20T11:53:35Z","_id":"1079","article_number":"6","oa":1,"publication_identifier":{"issn":["13850172"]},"status":"public","month":"06","publication":"Mathematical Physics, Analysis and Geometry","date_created":"2018-12-11T11:50:02Z","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publist_id":"6300","volume":20,"quality_controlled":"1","external_id":{"isi":["000401270000004"]},"day":"01","isi":1,"author":[{"full_name":"Nam, Phan","first_name":"Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Den Bosch, Hanne","first_name":"Hanne","last_name":"Van Den Bosch"}],"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer"},{"title":"Reconstructing metastatic seeding patterns of human cancers","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"31","file":[{"relation":"main_file","content_type":"application/pdf","file_size":897050,"file_id":"5133","creator":"system","access_level":"open_access","date_updated":"2018-12-12T10:15:15Z","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","date_created":"2018-12-12T10:15:15Z"}],"isi":1,"author":[{"first_name":"Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"full_name":"Makohon Moore, Alvin","first_name":"Alvin","last_name":"Makohon Moore"},{"first_name":"Jeffrey","last_name":"Gerold","full_name":"Gerold, Jeffrey"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Christine","last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"article_processing_charge":"No","pubrep_id":"786","publist_id":"6301","volume":8,"quality_controlled":"1","external_id":{"isi":["000393096600001"]},"publication":"Nature Communications","date_created":"2018-12-11T11:50:02Z","has_accepted_license":"1","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"journal_article","oa":1,"publication_identifier":{"issn":["20411723"]},"status":"public","ec_funded":1,"month":"01","year":"2017","abstract":[{"lang":"eng","text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods."}],"date_updated":"2023-09-20T11:55:31Z","_id":"1080","article_number":"14114","ddc":["004","006"],"file_date_updated":"2018-12-12T10:15:15Z","scopus_import":"1","intvolume":"         8","citation":{"mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>"},"doi":"10.1038/ncomms14114","publication_status":"published","date_published":"2017-01-31T00:00:00Z","oa_version":"Published Version"},{"day":"01","isi":1,"author":[{"full_name":"Fang, Chong","last_name":"Fang","first_name":"Chong"},{"full_name":"Nagy-Staron, Anna A","first_name":"Anna A","orcid":"0000-0002-1391-8377","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grafe, Martin","last_name":"Grafe","first_name":"Martin"},{"full_name":"Heermann, Ralf","first_name":"Ralf","last_name":"Heermann"},{"last_name":"Jung","first_name":"Kirsten","full_name":"Jung, Kirsten"},{"first_name":"Susanne","last_name":"Gebhard","full_name":"Gebhard, Susanne"},{"first_name":"Thorsten","last_name":"Mascher","full_name":"Mascher, Thorsten"}],"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","publisher":"Wiley-Blackwell","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:50:03Z","page":"16 - 31","publication":"Molecular Microbiology","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"type":"journal_article","publist_id":"6294","article_processing_charge":"No","external_id":{"isi":["000398059200002"]},"quality_controlled":"1","volume":104,"year":"2017","date_updated":"2023-09-20T11:48:43Z","issue":"1","abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"_id":"1084","publication_identifier":{"issn":[" 0950382X"]},"status":"public","month":"04","publication_status":"published","doi":"10.1111/mmi.13597","date_published":"2017-04-01T00:00:00Z","oa_version":"None","scopus_import":"1","citation":{"short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","ieee":"C. Fang <i>et al.</i>, “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” <i>Molecular Microbiology</i>, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. 2017;104(1):16-31. doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., &#38; Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>.","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>."},"intvolume":"       104"}]