[{"language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2017.09.006","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"11","volume":113,"date_created":"2018-12-11T11:46:33Z","date_updated":"2021-01-12T07:59:28Z","author":[{"full_name":"Fallesen, Todd","last_name":"Fallesen","first_name":"Todd"},{"full_name":"Roostalu, Johanna","last_name":"Roostalu","first_name":"Johanna"},{"full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","first_name":"Christian F"},{"first_name":"Gunnar","last_name":"Pruessner","full_name":"Pruessner, Gunnar"},{"full_name":"Surrey, Thomas","first_name":"Thomas","last_name":"Surrey"}],"department":[{"_id":"MaLo"}],"publisher":"Biophysical Society","publication_status":"published","year":"2017","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","publist_id":"7369","file_date_updated":"2020-07-14T12:46:31Z","date_published":"2017-11-07T00:00:00Z","page":"2055 - 2067","article_type":"original","citation":{"ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006.","chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006."},"publication":"Biophysical Journal","article_processing_charge":"No","has_accepted_license":"1","day":"07","file":[{"file_id":"5052","relation":"main_file","date_updated":"2020-07-14T12:46:31Z","date_created":"2018-12-12T10:14:03Z","checksum":"99a2474088e20ac74b1882c4fbbb45b1","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":977192}],"oa_version":"Published Version","pubrep_id":"965","intvolume":" 113","status":"public","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"453","issue":"9","abstract":[{"lang":"eng","text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor."}],"type":"journal_article"},{"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-09-26T00:00:00Z","publication":"Logical Methods in Computer Science","citation":{"ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26.","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017","mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017).","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017."},"abstract":[{"lang":"eng","text":"The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years."}],"issue":"3","type":"journal_article","pubrep_id":"956","file":[{"file_name":"IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf","access_level":"open_access","content_type":"application/pdf","file_size":582940,"creator":"system","relation":"main_file","file_id":"5010","date_updated":"2020-07-14T12:46:32Z","date_created":"2018-12-12T10:13:27Z","checksum":"12d469ae69b80361333d7dead965cf5d"}],"oa_version":"Published Version","_id":"464","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"Improved algorithms for parity and Streett objectives","status":"public","intvolume":" 13","month":"09","publication_identifier":{"issn":["1860-5974"]},"doi":"10.23638/LMCS-13(3:26)2017","language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"arxiv":["1410.0833"]},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"file_date_updated":"2020-07-14T12:46:32Z","ec_funded":1,"publist_id":"7357","license":"https://creativecommons.org/licenses/by-nd/4.0/","article_number":"26","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"}],"related_material":{"record":[{"id":"1661","status":"public","relation":"earlier_version"}]},"date_updated":"2023-02-23T10:08:55Z","date_created":"2018-12-11T11:46:37Z","volume":13,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic"},{"scopus_import":1,"day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication":"ACM Transactions on Graphics","citation":{"ama":"Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103.","apa":"Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017.","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678."},"article_type":"original","date_published":"2017-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.","lang":"eng"}],"issue":"4","_id":"470","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["006"],"title":"Water wave packets","status":"public","intvolume":" 36","file":[{"file_name":"wavepackets_final.pdf","access_level":"open_access","creator":"wojtan","content_type":"application/pdf","file_size":13131683,"file_id":"7359","relation":"main_file","date_created":"2020-01-24T09:32:35Z","date_updated":"2020-07-14T12:46:34Z","checksum":"82a3b2bfeee4ddef16ecc21675d1a48a"}],"oa_version":"Published Version","month":"07","publication_identifier":{"issn":["07300301"]},"oa":1,"quality_controlled":"1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/3072959.3073678","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"article_number":"103","file_date_updated":"2020-07-14T12:46:34Z","ec_funded":1,"publist_id":"7350","year":"2017","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","first_name":"Stefan","full_name":"Jeschke, Stefan"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-02-23T12:20:26Z","date_created":"2018-12-11T11:46:39Z","volume":36},{"date_published":"2017-05-01T00:00:00Z","publication":"ACM Transactions on Computational Logic (TOCL)","citation":{"ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 18(2), 12.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139."},"day":"01","scopus_import":1,"oa_version":"Submitted Version","title":"Faster statistical model checking for unbounded temporal properties","status":"public","intvolume":" 18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"471","abstract":[{"text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. ","lang":"eng"}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1145/3060139","quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"oa":1,"month":"05","publication_identifier":{"issn":["15293785"]},"date_created":"2018-12-11T11:46:39Z","date_updated":"2023-02-21T16:48:11Z","volume":18,"author":[{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905"}],"related_material":{"record":[{"id":"1234","relation":"earlier_version","status":"public"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"year":"2017","ec_funded":1,"publist_id":"7349","article_number":"12"},{"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10892"}]},"author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"full_name":"Huber, Stefan","first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814"},{"first_name":"Peter","last_name":"Palfrader","full_name":"Palfrader, Peter"}],"volume":26,"date_created":"2018-12-11T11:46:43Z","date_updated":"2023-02-21T16:06:22Z","year":"2017","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","department":[{"_id":"HeEd"}],"publisher":"World Scientific Publishing","publication_status":"published","publist_id":"7338","file_date_updated":"2020-07-14T12:46:35Z","doi":"10.1142/S0218195916600050","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"04","pubrep_id":"949","file":[{"access_level":"open_access","file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","content_type":"application/pdf","file_size":769296,"creator":"system","relation":"main_file","file_id":"4758","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","date_created":"2018-12-12T10:09:34Z","date_updated":"2020-07-14T12:46:35Z"}],"oa_version":"Published Version","_id":"481","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 26","status":"public","title":"Planar matchings for weighted straight skeletons","ddc":["004","514","516"],"issue":"3-4","abstract":[{"lang":"eng","text":"We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings."}],"type":"journal_article","date_published":"2017-04-13T00:00:00Z","citation":{"mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050.","short":"T. Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050.","ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229. doi:10.1142/S0218195916600050","ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. 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Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4","ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4","chicago":"Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.","mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738."},"publication":"Advances in Theoretical and Mathematical Physics","date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 21","title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","status":"public","_id":"484","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory."}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1509.04631","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.4310/ATMP.2017.v21.n3.a4","publication_identifier":{"issn":["10950761"]},"month":"01","department":[{"_id":"RoSe"}],"publisher":"International Press","publication_status":"published","year":"2017","volume":21,"date_updated":"2021-01-12T08:00:58Z","date_created":"2018-12-11T11:46:43Z","author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","first_name":"Phan","full_name":"Nam, Phan"},{"full_name":"Napiórkowski, Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","first_name":"Marcin M"}],"ec_funded":1,"publist_id":"7336"},{"page":"739 - 800","publication":"Advances in Theoretical and Mathematical Physics","citation":{"ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5","chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.","mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800."},"date_published":"2017-08-25T00:00:00Z","scopus_import":1,"day":"25","title":"Universality for a class of random band matrices","status":"public","intvolume":" 21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"483","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices."}],"issue":"3","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02312"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.4310/ATMP.2017.v21.n3.a5","month":"08","publication_identifier":{"issn":["10950761"]},"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"International Press","year":"2017","date_created":"2018-12-11T11:46:43Z","date_updated":"2021-01-12T08:00:57Z","volume":21,"author":[{"last_name":"Bourgade","first_name":"Paul","full_name":"Bourgade, Paul"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng"},{"last_name":"Yin","first_name":"Jun","full_name":"Yin, Jun"}],"publist_id":"7337","ec_funded":1},{"type":"conference","abstract":[{"text":"In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x.","lang":"eng"}],"publist_id":"7333","publication_status":"published","title":"Towards unlicensed cellular networks in TV white spaces","status":"public","department":[{"_id":"DaAl"}],"publisher":"ACM","_id":"487","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:21:11Z","date_created":"2018-12-11T11:46:45Z","oa_version":"None","author":[{"full_name":"Baig, Ghufran","last_name":"Baig","first_name":"Ghufran"},{"last_name":"Radunovic","first_name":"Bozidar","full_name":"Radunovic, Bozidar"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Balkwill","first_name":"Matthew","full_name":"Balkwill, Matthew"},{"first_name":"Thomas","last_name":"Karagiannis","full_name":"Karagiannis, Thomas"},{"full_name":"Qiu, Lili","first_name":"Lili","last_name":"Qiu"}],"scopus_import":1,"day":"28","month":"11","publication_identifier":{"isbn":["978-145035422-6"]},"quality_controlled":"1","page":"2 - 14","publication":"Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies","citation":{"short":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14.","mla":"Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.","chicago":"Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367.","ama":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367","ieee":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14.","apa":"Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367","ista":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14."},"language":[{"iso":"eng"}],"conference":{"start_date":"2017-12-12","location":"Incheon, South Korea","end_date":"2017-12-15","name":"CoNEXT: Conference on emerging Networking EXperiments and Technologies"},"date_published":"2017-11-28T00:00:00Z","doi":"10.1145/3143361.3143367"},{"publist_id":"7305","file_date_updated":"2020-07-14T12:46:36Z","article_number":"16032","author":[{"full_name":"Simonnet, Jean","first_name":"Jean","last_name":"Simonnet"},{"last_name":"Nassar","first_name":"Mérie","full_name":"Nassar, Mérie"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","first_name":"Federico","last_name":"Stella","full_name":"Stella, Federico"},{"last_name":"Cohen","first_name":"Ivan","full_name":"Cohen, Ivan"},{"last_name":"Mathon","first_name":"Bertrand","full_name":"Mathon, Bertrand"},{"first_name":"Charlotte","last_name":"Boccara","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte"},{"full_name":"Miles, Richard","last_name":"Miles","first_name":"Richard"},{"full_name":"Fricker, Desdemona","first_name":"Desdemona","last_name":"Fricker"}],"volume":8,"date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:16Z","year":"2017","department":[{"_id":"JoCs"}],"publisher":"Nature Publishing Group","publication_status":"published","publication_identifier":{"issn":["20411723"]},"month":"07","doi":"10.1038/ncomms16032","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum."}],"type":"journal_article","pubrep_id":"937","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","content_type":"application/pdf","file_size":2948357,"creator":"system","relation":"main_file","file_id":"5083","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","date_created":"2018-12-12T10:14:31Z","date_updated":"2020-07-14T12:46:36Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"514","intvolume":" 8","title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","ddc":["571"],"status":"public","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-07-01T00:00:00Z","citation":{"ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032."},"publication":"Nature Communications"},{"file":[{"file_size":4118385,"content_type":"application/pdf","creator":"lsazanov","file_name":"29893_2_merged_1501257589_red.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z","date_created":"2019-11-07T12:51:07Z","checksum":"9bc7e8c41b43636dd7566289e511f096","relation":"main_file","file_id":"6993"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"515","intvolume":" 24","ddc":["572"],"title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","status":"public","issue":"10","abstract":[{"text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.","lang":"eng"}],"type":"journal_article","date_published":"2017-10-05T00:00:00Z","citation":{"chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808.","ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460"},"publication":"Nature Structural and Molecular Biology","page":"800 - 808","article_type":"original","has_accepted_license":"1","day":"05","scopus_import":1,"author":[{"last_name":"Letts","first_name":"James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","full_name":"Letts, James A"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"volume":24,"date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:17Z","year":"2017","department":[{"_id":"LeSa"}],"publisher":"Nature Publishing Group","publication_status":"published","publist_id":"7304","ec_funded":1,"file_date_updated":"2020-07-14T12:46:36Z","doi":"10.1038/nsmb.3460","language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"quality_controlled":"1","publication_identifier":{"issn":["15459993"]},"month":"10"},{"month":"04","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.2.043904","date_published":"2017-04-01T00:00:00Z","quality_controlled":"1","citation":{"chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904.","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904"},"main_file_link":[{"url":"https://arxiv.org/abs/1704.02619","open_access":"1"}],"oa":1,"publication":"Physical Review Fluids","issue":"4","publist_id":"7306","abstract":[{"lang":"eng","text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction."}],"type":"journal_article","article_number":"043904","volume":2,"oa_version":"Preprint","date_created":"2018-12-11T11:46:54Z","date_updated":"2021-01-12T08:01:16Z","author":[{"full_name":"Klotz, Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1740-7635","first_name":"Lukasz","last_name":"Klotz"},{"last_name":"Lemoult","first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M"},{"last_name":"Frontczak","first_name":"Idalia","full_name":"Frontczak, Idalia"},{"full_name":"Tuckerman, Laurette","last_name":"Tuckerman","first_name":"Laurette"},{"full_name":"Wesfreid, José","first_name":"José","last_name":"Wesfreid"}],"publisher":"American Physical Society","department":[{"_id":"BjHo"}],"intvolume":" 2","publication_status":"published","status":"public","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","_id":"513","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_type":"letter_note","page":"395 - 401","publication":"ACS Synthetic Biology","citation":{"chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.","mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","ieee":"W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017.","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235","ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235"},"date_published":"2017-03-17T00:00:00Z","scopus_import":1,"day":"17","status":"public","title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"520","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here."}],"issue":"3","quality_controlled":"1","external_id":{"pmid":["27936615"]},"language":[{"iso":"eng"}],"doi":"10.1021/acssynbio.6b00235","month":"03","publication_identifier":{"issn":["21615063"]},"publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"American Chemical Society","year":"2017","pmid":1,"date_created":"2018-12-11T11:46:56Z","date_updated":"2021-01-12T08:01:21Z","volume":6,"author":[{"first_name":"Wei","last_name":"Du","full_name":"Du, Wei"},{"id":"4677C796-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8619-2223","first_name":"Andreas","last_name":"Angermayr","full_name":"Angermayr, Andreas"},{"full_name":"Jongbloets, Joeri","first_name":"Joeri","last_name":"Jongbloets"},{"full_name":"Molenaar, Douwe","last_name":"Molenaar","first_name":"Douwe"},{"first_name":"Herwig","last_name":"Bachmann","full_name":"Bachmann, Herwig"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"},{"full_name":"Branco Dos Santos, Filipe","first_name":"Filipe","last_name":"Branco Dos Santos"}],"publist_id":"7298"},{"quality_controlled":"1","page":"45 - 57","publication":"Topology and its Applications","citation":{"ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005","chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.03954v1"}],"oa":1,"language":[{"iso":"eng"}],"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","month":"01","day":"01","publication_identifier":{"issn":["01668641"]},"publication_status":"published","status":"public","title":"Higson compactification and dimension raising","intvolume":" 215","department":[{"_id":"HeEd"}],"publisher":"Elsevier","_id":"521","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:56Z","date_updated":"2021-01-12T08:01:21Z","oa_version":"Submitted Version","volume":215,"author":[{"full_name":"Austin, Kyle","first_name":"Kyle","last_name":"Austin"},{"id":"2E36B656-F248-11E8-B48F-1D18A9856A87","last_name":"Virk","first_name":"Ziga","full_name":"Virk, Ziga"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension."}],"publist_id":"7299"},{"publist_id":"7283","year":"2017","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer","author":[{"last_name":"Burton","first_name":"Benjamin","full_name":"Burton, Benjamin"},{"full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay","first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"1379","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:47:01Z","date_updated":"2023-02-21T17:01:34Z","volume":58,"month":"06","publication_identifier":{"issn":["01795376"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07907"}],"external_id":{"arxiv":["1602.07907"]},"quality_controlled":"1","doi":"10.1007/s00454-017-9900-0","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"issue":"4","_id":"534","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Finding non-orientable surfaces in 3-Manifolds","status":"public","intvolume":" 58","oa_version":"Preprint","scopus_import":1,"day":"09","article_processing_charge":"No","publication":"Discrete & Computational Geometry","citation":{"ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0."},"article_type":"original","page":"871 - 888","date_published":"2017-06-09T00:00:00Z"},{"page":"4679 - 4682","citation":{"mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998"},"publication":"Angewandte Chemie","date_published":"2017-05-20T00:00:00Z","has_accepted_license":"1","day":"20","intvolume":" 129","ddc":["571"],"title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"538","file":[{"file_id":"5007","relation":"main_file","date_created":"2018-12-12T10:13:24Z","date_updated":"2020-07-14T12:46:39Z","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1668557}],"oa_version":"Published Version","pubrep_id":"932","type":"journal_article","issue":"16","abstract":[{"lang":"ger","text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. "}],"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/ange.201611998","month":"05","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publisher":"Wiley","publication_status":"published","year":"2017","volume":129,"date_updated":"2021-01-12T08:01:33Z","date_created":"2018-12-11T11:47:02Z","author":[{"last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"last_name":"Stadler","first_name":"Manuela","full_name":"Stadler, Manuela"},{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"Distel, Martin","last_name":"Distel","first_name":"Martin"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"ec_funded":1,"publist_id":"7279","file_date_updated":"2020-07-14T12:46:39Z"},{"publist_id":"7276","file_date_updated":"2020-07-14T12:46:44Z","article_number":"e1006758","author":[{"full_name":"Khamina, Kseniya","last_name":"Khamina","first_name":"Kseniya"},{"full_name":"Lercher, Alexander","first_name":"Alexander","last_name":"Lercher"},{"first_name":"Michael","last_name":"Caldera","full_name":"Caldera, Michael"},{"last_name":"Schliehe","first_name":"Christopher","full_name":"Schliehe, Christopher"},{"last_name":"Vilagos","first_name":"Bojan","full_name":"Vilagos, Bojan"},{"first_name":"Mehmet","last_name":"Sahin","full_name":"Sahin, Mehmet"},{"last_name":"Kosack","first_name":"Lindsay","full_name":"Kosack, Lindsay"},{"first_name":"Anannya","last_name":"Bhattacharya","full_name":"Bhattacharya, Anannya"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"full_name":"Stukalov, Alexey","first_name":"Alexey","last_name":"Stukalov"},{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"full_name":"James, Leo","last_name":"James","first_name":"Leo"},{"full_name":"Pinschewer, Daniel","first_name":"Daniel","last_name":"Pinschewer"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"full_name":"Menche, Jörg","first_name":"Jörg","last_name":"Menche"},{"full_name":"Bergthaler, Andreas","first_name":"Andreas","last_name":"Bergthaler"}],"volume":13,"date_updated":"2021-01-12T08:01:48Z","date_created":"2018-12-11T11:47:03Z","year":"2017","department":[{"_id":"GaNo"}],"publisher":"Public Library of Science","publication_status":"published","publication_identifier":{"issn":["15537366"]},"month":"12","doi":"10.1371/journal.ppat.1006758","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","issue":"12","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"type":"journal_article","pubrep_id":"931","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4944","date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-12T10:12:26Z","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4106772,"creator":"system"}],"_id":"540","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","status":"public","ddc":["576","616"],"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-12-01T00:00:00Z","citation":{"chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758"},"publication":"PLoS Pathogens"},{"file":[{"content_type":"application/pdf","file_size":511832,"creator":"system","access_level":"open_access","file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","checksum":"bfa405385ec6229ad5ead89ab5751639","date_created":"2018-12-12T10:18:32Z","date_updated":"2020-07-14T12:46:33Z","relation":"main_file","file_id":"5354"}],"oa_version":"Published Version","pubrep_id":"957","intvolume":" 13","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","ddc":["004"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"466","issue":"2","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. "}],"type":"journal_article","date_published":"2017-07-03T00:00:00Z","citation":{"mla":"Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","chicago":"Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017.","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017","ista":"Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15.","ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017"},"publication":"Logical Methods in Computer Science","has_accepted_license":"1","day":"03","scopus_import":1,"volume":13,"date_created":"2018-12-11T11:46:38Z","date_updated":"2023-02-23T12:26:16Z","related_material":{"record":[{"id":"1657","status":"public","relation":"earlier_version"},{"id":"5429","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"5435"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Křetínská, Zuzana","last_name":"Křetínská","first_name":"Zuzana"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"}],"department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","publication_status":"published","year":"2017","ec_funded":1,"publist_id":"7355","file_date_updated":"2020-07-14T12:46:33Z","article_number":"15","language":[{"iso":"eng"}],"doi":"10.23638/LMCS-13(2:15)2017","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","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"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"publication_identifier":{"issn":["18605974"]},"month":"07"},{"month":"12","publication_identifier":{"issn":["15293785"]},"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"external_id":{"arxiv":["1606.03598"]},"main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1145/3152769","article_number":"31","publist_id":"7354","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"ACM","year":"2017","date_created":"2018-12-11T11:46:38Z","date_updated":"2023-02-23T12:26:19Z","volume":18,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1656","status":"public","relation":"earlier_version"},{"id":"5415","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5436"}]},"scopus_import":1,"day":"01","publication":"ACM Transactions on Computational Logic (TOCL)","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769."},"date_published":"2017-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.","lang":"eng"}],"issue":"4","title":"Nested weighted automata","status":"public","intvolume":" 18","_id":"467","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"_id":"465","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"Edit distance for pushdown automata","status":"public","intvolume":" 13","pubrep_id":"955","file":[{"file_size":279071,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2015-321-v1+1_main.pdf","checksum":"08041379ba408d40664f449eb5907a8f","date_created":"2018-12-12T10:14:37Z","date_updated":"2020-07-14T12:46:33Z","relation":"main_file","file_id":"5090"},{"creator":"system","file_size":279071,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","checksum":"08041379ba408d40664f449eb5907a8f","date_updated":"2020-07-14T12:46:33Z","date_created":"2018-12-12T10:14:38Z","file_id":"5091","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ","lang":"eng"}],"issue":"3","publication":"Logical Methods in Computer Science","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). 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The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. 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Nature Publishing Group, 2017.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w."},"file_date_updated":"2020-07-14T12:46:36Z","ec_funded":1,"publist_id":"7307","article_number":"82","author":[{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5449"}]},"date_updated":"2023-02-23T12:26:57Z","date_created":"2018-12-11T11:46:53Z","volume":7,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","month":"03","publication_identifier":{"issn":["20452322"]},"doi":"10.1038/s41598-017-00107-w","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}]}]