[{"date_created":"2018-12-11T11:44:57Z","doi":"10.1038/s41467-018-05417-9","date_published":"2018-07-30T00:00:00Z","publication":"Nature Communications","day":"30","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","title":"Statistical mechanics for metabolic networks during steady state growth","external_id":{"isi":["000440149300021"]},"article_processing_charge":"No","publist_id":"7760","author":[{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"last_name":"Mc","full_name":"Mc, Andersson Anna","first_name":"Andersson Anna"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9."},"project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"2988","ec_funded":1,"related_material":{"record":[{"relation":"popular_science","id":"5587","status":"public"}]},"issue":"1","volume":9,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:06Z","file_size":1043205,"creator":"dernst","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5728","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18"}],"publication_status":"published","intvolume":" 9","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:06Z","ddc":["570"],"date_updated":"2024-02-21T13:45:39Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"161"},{"page":"365 - 375","doi":"10.1534/genetics.117.300513","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:04Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"publist_id":"7274","external_id":{"isi":["000419356300024"]},"article_processing_charge":"No","title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","citation":{"chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","apa":"Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"related_material":{"record":[{"id":"5571","status":"public","relation":"popular_science"},{"relation":"popular_science","status":"public","id":"5572"}]},"volume":208,"issue":"1","ec_funded":1,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"2123845e7031a0cf043905be160f9e69","file_id":"5132","creator":"system","file_size":1311661,"date_updated":"2020-07-14T12:46:50Z","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","date_created":"2018-12-12T10:15:14Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 208","abstract":[{"lang":"eng","text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter."}],"oa_version":"Published Version","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:46:50Z","date_updated":"2024-02-21T13:48:27Z","ddc":["576"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"1058","_id":"542"},{"month":"06","intvolume":" 1","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures."}],"related_material":{"record":[{"status":"public","id":"7196","relation":"part_of_dissertation"},{"relation":"popular_science","status":"public","id":"5559"}]},"issue":"1","volume":1,"ec_funded":1,"file":[{"date_created":"2018-12-18T13:37:04Z","file_name":"2018_CommBiology_Pavlogiannis.pdf","date_updated":"2020-07-14T12:47:10Z","file_size":1804194,"creator":"dernst","checksum":"a9db825fa3b64a51ff3de035ec973b3e","file_id":"5752","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2399-3642"]},"publication_status":"published","status":"public","pubrep_id":"1045","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"5751","file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"KrCh"}],"ddc":["004","519","576"],"date_updated":"2024-02-21T13:48:42Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"doi":"10.1038/s42003-018-0078-7","date_published":"2018-06-14T00:00:00Z","date_created":"2018-12-18T13:22:58Z","day":"14","publication":"Communications Biology","has_accepted_license":"1","isi":1,"year":"2018","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_number":"71","title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","author":[{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"external_id":{"isi":["000461126500071"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71."}},{"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:44:57Z","date_updated":"2024-02-22T14:34:33Z","supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"}],"ddc":["515","519"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","pubrep_id":"1040","status":"public","_id":"149","ec_funded":1,"related_material":{"record":[{"status":"public","id":"1677","relation":"part_of_dissertation"},{"id":"550","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6183"},{"status":"public","id":"566","relation":"part_of_dissertation"},{"status":"public","id":"1010","relation":"part_of_dissertation"},{"status":"public","id":"6240","relation":"part_of_dissertation"},{"status":"public","id":"6184","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-04-08T13:55:20Z","file_name":"2018_thesis_Alt.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:57Z","file_size":5801709,"checksum":"d4dad55a7513f345706aaaba90cb1bb8","file_id":"6241","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"checksum":"d73fcf46300dce74c403f2b491148ab4","file_id":"6242","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2019-04-08T13:55:20Z","file_name":"2018_thesis_Alt_source.zip","date_updated":"2020-07-14T12:44:57Z","file_size":3802059,"creator":"dernst"}],"alternative_title":["ISTA Thesis"],"month":"07","abstract":[{"text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","publist_id":"7772","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes","last_name":"Alt"}],"title":"Dyson equation and eigenvalue statistics of random matrices","citation":{"ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040","apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040","mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"456","date_created":"2018-12-11T11:44:53Z","date_published":"2018-07-12T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1040","year":"2018","has_accepted_license":"1","day":"12","oa":1,"publisher":"Institute of Science and Technology Austria"},{"acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","publication":"The Journal of Chemical Physics","day":"14","year":"2018","isi":1,"date_created":"2018-12-11T11:46:21Z","doi":"10.1063/1.5017591","date_published":"2018-03-14T00:00:00Z","article_number":"104307","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591.","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307."},"title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","external_id":{"isi":["000427517200065"],"arxiv":["1711.09904"]},"article_processing_charge":"No","author":[{"first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7408","oa_version":"Preprint","abstract":[{"text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.","lang":"eng"}],"intvolume":" 148","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09904"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":148,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"issue":"10","_id":"415","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-02-28T13:01:59Z","department":[{"_id":"MiLe"}]},{"issue":"4","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","relation":"press_release"}]},"volume":37,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5744","checksum":"db75ebabe2ec432bf41389e614d6ef62","creator":"dernst","date_updated":"2020-07-14T12:44:45Z","file_size":22185016,"date_created":"2018-12-18T09:59:23Z","file_name":"2018_ACM_Jeschke.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 37","scopus_import":"1","alternative_title":["SIGGRAPH"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:44:45Z","ddc":["000"],"date_updated":"2024-02-28T13:58:51Z","status":"public","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"134","date_published":"2018-07-30T00:00:00Z","doi":"10.1145/3197517.3201336","date_created":"2018-12-11T11:44:48Z","day":"30","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2018","publisher":"ACM","quality_controlled":"1","oa":1,"title":"Water surface wavelets","author":[{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan","last_name":"Jeschke"},{"first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas","last_name":"Skrivan"},{"last_name":"Mueller Fischer","full_name":"Mueller Fischer, Matthias","first_name":"Matthias"},{"first_name":"Nuttapong","full_name":"Chentanez, Nuttapong","last_name":"Chentanez"},{"first_name":"Miles","last_name":"Macklin","full_name":"Macklin, Miles"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publist_id":"7789","article_processing_charge":"No","external_id":{"isi":["000448185000055"]},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94."},"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"article_number":"94"},{"article_processing_charge":"No","external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"author":[{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"first_name":"Timur","last_name":"Tscherbul","full_name":"Tscherbul, Timur"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","citation":{"ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"article_number":"165301","date_created":"2019-04-17T10:53:38Z","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/physrevlett.121.165301","year":"2018","isi":1,"publication":"Physical Review Letters","day":"16","oa":1,"quality_controlled":"1","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:15:09Z","type":"journal_article","status":"public","_id":"6339","volume":121,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","description":"News on IST Homepage"}]},"issue":"16","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"scopus_import":"1","intvolume":" 121","month":"10","abstract":[{"text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment.","lang":"eng"}],"oa_version":"Preprint"},{"date_updated":"2024-02-28T13:14:53Z","department":[{"_id":"MiLe"}],"_id":"417","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"16","volume":121,"oa_version":"Preprint","abstract":[{"text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ","lang":"eng"}],"intvolume":" 121","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301."},"title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","external_id":{"arxiv":["1803.07990"]},"article_processing_charge":"No","publist_id":"8025","author":[{"last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Timur","full_name":"Tscherbul, Timur","last_name":"Tscherbul"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"article_number":"165301","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"publication":"Physical Review Letters","day":"16","year":"2018","date_created":"2018-12-11T11:46:22Z","doi":"10.1103/PhysRevLett.121.165301","date_published":"2018-10-16T00:00:00Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1"},{"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785."},"title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","external_id":{"isi":["000429441400018"],"pmid":["29511054"]},"article_processing_charge":"No","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"},{"first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"7417","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","publication":"The Plant Cell","day":"09","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:46:20Z","date_published":"2018-04-09T00:00:00Z","doi":"10.1105/tpc.17.00785","page":"700 - 716","_id":"412","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2024-03-27T23:30:06Z","department":[{"_id":"JiFr"}],"file_date_updated":"2022-05-23T09:12:38Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"intvolume":" 30","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"11406","checksum":"4e165e653b67d3f0684697f21aace5a1","file_size":4407538,"date_updated":"2022-05-23T09:12:38Z","creator":"dernst","file_name":"2018_PlantCell_Adamowski.pdf","date_created":"2022-05-23T09:12:38Z"}],"publication_status":"published","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"ec_funded":1,"volume":30,"issue":"3","related_material":{"record":[{"id":"6269","status":"public","relation":"dissertation_contains"}]}},{"date_published":"2018-07-27T00:00:00Z","doi":"10.1523/ENEURO.0087-18.2018","date_created":"2019-02-03T22:59:16Z","day":"27","publication":"eNeuro","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Society of Neuroscience","oa":1,"title":"Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning","author":[{"last_name":"Rangel Guerrero","orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James G.","last_name":"Donnett","full_name":"Donnett, James G."},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"},{"last_name":"Kovács","full_name":"Kovács, Krisztián","orcid":"0000-0001-6251-1007","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián"}],"article_processing_charge":"No","external_id":{"isi":["000443994700007"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Rangel Guerrero, Dámaris K., et al. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro, vol. 5, no. 4, e0087, Society of Neuroscience, 2018, doi:10.1523/ENEURO.0087-18.2018.","apa":"Rangel Guerrero, D. K., Donnett, J. G., Csicsvari, J. L., & Kovács, K. (2018). Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. ENeuro. Society of Neuroscience. https://doi.org/10.1523/ENEURO.0087-18.2018","ama":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 2018;5(4). doi:10.1523/ENEURO.0087-18.2018","ieee":"D. K. Rangel Guerrero, J. G. Donnett, J. L. Csicsvari, and K. Kovács, “Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning,” eNeuro, vol. 5, no. 4. Society of Neuroscience, 2018.","short":"D.K. Rangel Guerrero, J.G. Donnett, J.L. Csicsvari, K. Kovács, ENeuro 5 (2018).","chicago":"Rangel Guerrero, Dámaris K, James G. Donnett, Jozsef L Csicsvari, and Krisztián Kovács. “Tetrode Recording from the Hippocampus of Behaving Mice Coupled with Four-Point-Irradiation Closed-Loop Optogenetics: A Technique to Study the Contribution of Hippocampal SWR Events to Learning.” ENeuro. Society of Neuroscience, 2018. https://doi.org/10.1523/ENEURO.0087-18.2018.","ista":"Rangel Guerrero DK, Donnett JG, Csicsvari JL, Kovács K. 2018. Tetrode recording from the hippocampus of behaving mice coupled with four-point-irradiation closed-loop optogenetics: A technique to study the contribution of Hippocampal SWR events to learning. eNeuro. 5(4), e0087."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"I2072-B27","name":"Interneuron plasticity during spatial learning","call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425"}],"article_number":"e0087","related_material":{"record":[{"relation":"dissertation_contains","id":"6849","status":"public"}]},"issue":"4","volume":5,"ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:13Z","file_size":3746884,"date_created":"2019-02-05T12:48:36Z","file_name":"2018_ENeuro_Guerrero.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f4915d45fc7ad4648b7b7a13fdecca01","file_id":"5921"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 5","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"With the advent of optogenetics, it became possible to change the activity of a targeted population of neurons in a temporally controlled manner. To combine the advantages of 60-channel in vivo tetrode recording and laser-based optogenetics, we have developed a closed-loop recording system that allows for the actual electrophysiological signal to be used as a trigger for the laser light mediating the optogenetic intervention. We have optimized the weight, size, and shape of the corresponding implant to make it compatible with the size, force, and movements of a behaving mouse, and we have shown that the system can efficiently block sharp wave ripple (SWR) events using those events themselves as a trigger. To demonstrate the full potential of the optogenetic recording system we present a pilot study addressing the contribution of SWR events to learning in a complex behavioral task."}],"department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:47:13Z","ddc":["570"],"date_updated":"2024-03-27T23:30:10Z","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"5914"}]