[{"oa":1,"publisher":"ACM","quality_controlled":"1","publication":"ACM Transactions on Computational Logic (TOCL)","day":"01","year":"2017","date_created":"2018-12-11T11:46:39Z","doi":"10.1145/3060139","date_published":"2017-05-01T00:00:00Z","article_number":"12","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017).","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","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","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.","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.","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."},"title":"Faster statistical model checking for unbounded temporal properties","publist_id":"7349","author":[{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"oa_version":"Submitted Version","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"}],"intvolume":" 18","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1504.05739","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["15293785"]},"ec_funded":1,"volume":18,"issue":"2","related_material":{"record":[{"relation":"earlier_version","id":"1234","status":"public"}]},"_id":"471","status":"public","type":"journal_article","date_updated":"2023-02-21T16:48:11Z","department":[{"_id":"ToHe"}]},{"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","pubrep_id":"949","status":"public","_id":"481","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:35Z","date_updated":"2023-02-21T16:06:22Z","ddc":["004","514","516"],"scopus_import":1,"intvolume":" 26","month":"04","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","volume":26,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10892"}]},"issue":"3-4","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":769296,"date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","date_created":"2018-12-12T10:09:34Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","file_id":"4758"}],"publist_id":"7338","author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","last_name":"Huber"},{"first_name":"Peter","full_name":"Palfrader, Peter","last_name":"Palfrader"}],"title":"Planar matchings for weighted straight skeletons","citation":{"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","apa":"Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050","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. World Scientific Publishing, pp. 211–229, 2017.","short":"T. Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","page":"211 - 229","date_created":"2018-12-11T11:46:43Z","doi":"10.1142/S0218195916600050","date_published":"2017-04-13T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"International Journal of Computational Geometry and Applications","day":"13"},{"title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","publist_id":"7336","author":[{"last_name":"Nam","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738.","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.","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","apa":"Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. 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"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-01-01T00:00:00Z","doi":"10.4310/ATMP.2017.v21.n3.a4","date_created":"2018-12-11T11:46:43Z","page":"683 - 738","day":"01","publication":"Advances in Theoretical and Mathematical Physics","year":"2017","quality_controlled":"1","publisher":"International Press","oa":1,"department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T08:00:58Z","status":"public","type":"journal_article","_id":"484","issue":"3","volume":21,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10950761"]},"publication_status":"published","month":"01","intvolume":" 21","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1509.04631","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}]},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02312"}],"scopus_import":1,"intvolume":" 21","month":"08","publication_status":"published","publication_identifier":{"issn":["10950761"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":21,"issue":"3","_id":"483","type":"journal_article","status":"public","date_updated":"2021-01-12T08:00:57Z","department":[{"_id":"LaEr"}],"oa":1,"publisher":"International Press","quality_controlled":"1","year":"2017","publication":"Advances in Theoretical and Mathematical Physics","day":"25","page":"739 - 800","date_created":"2018-12-11T11:46:43Z","doi":"10.4310/ATMP.2017.v21.n3.a5","date_published":"2017-08-25T00:00:00Z","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"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.","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.","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","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.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bourgade, Paul","last_name":"Bourgade","first_name":"Paul"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"last_name":"Yau","full_name":"Yau, Horng","first_name":"Horng"},{"full_name":"Yin, Jun","last_name":"Yin","first_name":"Jun"}],"publist_id":"7337","title":"Universality for a class of random band matrices"},{"scopus_import":1,"month":"07","intvolume":" 8","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."}],"oa_version":"Published Version","volume":8,"publication_identifier":{"issn":["20411723"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:14:31Z","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","date_updated":"2020-07-14T12:46:36Z","file_size":2948357,"creator":"system","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","file_id":"5083","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"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":"937","_id":"514","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"JoCs"}],"date_updated":"2021-01-12T08:01:16Z","ddc":["571"],"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"doi":"10.1038/ncomms16032","date_published":"2017-07-01T00:00:00Z","date_created":"2018-12-11T11:46:54Z","has_accepted_license":"1","year":"2017","day":"01","publication":"Nature Communications","article_number":"16032","publist_id":"7305","author":[{"first_name":"Jean","last_name":"Simonnet","full_name":"Simonnet, Jean"},{"full_name":"Nassar, Mérie","last_name":"Nassar","first_name":"Mérie"},{"full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cohen, Ivan","last_name":"Cohen","first_name":"Ivan"},{"first_name":"Bertrand","last_name":"Mathon","full_name":"Mathon, Bertrand"},{"full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","last_name":"Boccara","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","first_name":"Charlotte"},{"first_name":"Richard","last_name":"Miles","full_name":"Miles, Richard"},{"first_name":"Desdemona","full_name":"Fricker, Desdemona","last_name":"Fricker"}],"title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","citation":{"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.","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","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","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"project":[{"call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","grant_number":"701309"}],"publist_id":"7304","author":[{"full_name":"Letts, James A","orcid":"0000-0002-9864-3586","last_name":"Letts","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","citation":{"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.","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.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","page":"800 - 808","date_created":"2018-12-11T11:46:54Z","date_published":"2017-10-05T00:00:00Z","doi":"10.1038/nsmb.3460","year":"2017","has_accepted_license":"1","publication":"Nature Structural and Molecular Biology","day":"05","type":"journal_article","article_type":"original","status":"public","_id":"515","department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:46:36Z","date_updated":"2021-01-12T08:01:17Z","ddc":["572"],"scopus_import":1,"intvolume":" 24","month":"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"}],"oa_version":"Submitted Version","ec_funded":1,"volume":24,"issue":"10","publication_status":"published","publication_identifier":{"issn":["15459993"]},"language":[{"iso":"eng"}],"file":[{"creator":"lsazanov","date_updated":"2020-07-14T12:46:36Z","file_size":4118385,"date_created":"2019-11-07T12:51:07Z","file_name":"29893_2_merged_1501257589_red.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6993","checksum":"9bc7e8c41b43636dd7566289e511f096"}]},{"publication":"Physical Review Fluids","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2017","date_created":"2018-12-11T11:46:54Z","date_published":"2017-04-01T00:00:00Z","issue":"4","doi":"10.1103/PhysRevFluids.2.043904","volume":2,"oa_version":"Preprint","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."}],"intvolume":" 2","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.02619"}],"oa":1,"publisher":"American Physical Society","quality_controlled":"1","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","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."},"date_updated":"2021-01-12T08:01:16Z","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","department":[{"_id":"BjHo"}],"author":[{"orcid":"0000-0003-1740-7635","full_name":"Klotz, Lukasz","last_name":"Klotz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz"},{"first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","last_name":"Lemoult","full_name":"Lemoult, Grégoire M"},{"first_name":"Idalia","full_name":"Frontczak, Idalia","last_name":"Frontczak"},{"last_name":"Tuckerman","full_name":"Tuckerman, Laurette","first_name":"Laurette"},{"first_name":"José","full_name":"Wesfreid, José","last_name":"Wesfreid"}],"publist_id":"7306","article_number":"043904","_id":"513","status":"public","type":"journal_article"},{"volume":215,"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","date_created":"2018-12-11T11:46:56Z","page":"45 - 57","day":"01","language":[{"iso":"eng"}],"publication":"Topology and its Applications","publication_identifier":{"issn":["01668641"]},"year":"2017","publication_status":"published","month":"01","intvolume":" 215","quality_controlled":"1","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.03954v1"}],"oa":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"Higson compactification and dimension raising","department":[{"_id":"HeEd"}],"publist_id":"7299","author":[{"last_name":"Austin","full_name":"Austin, Kyle","first_name":"Kyle"},{"full_name":"Virk, Ziga","last_name":"Virk","first_name":"Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:01:21Z","citation":{"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.","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","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.","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","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","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017."},"status":"public","type":"journal_article","_id":"521"},{"type":"journal_article","status":"public","pubrep_id":"983","_id":"525","publist_id":"7294","author":[{"last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","full_name":"Daniel von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"Tatsuaki","last_name":"Goh","full_name":"Goh, Tatsuaki"},{"first_name":"Daniela","full_name":"Dietrich, Daniela","last_name":"Dietrich"},{"first_name":"Malcolm","full_name":"Bennett, Malcolm J","last_name":"Bennett"}],"file_date_updated":"2020-07-14T12:46:38Z","title":"Plant biology: Building barriers… in roots","date_updated":"2021-01-12T08:01:23Z","citation":{"ista":"von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building barriers… in roots. Current Biology. 27(5), R172–R174.","chicago":"Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett. “Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.01.060.","ama":"von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers… in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060","apa":"von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060","ieee":"D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174, 2017.","short":"D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017) R172–R174.","mla":"von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.” Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060."},"extern":1,"quality_controlled":0,"publisher":"Cell Press","main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/983","open_access":"1"}],"oa":1,"month":"03","intvolume":" 27","abstract":[{"text":"The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. ","lang":"eng"}],"acknowledgement":"Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1 and BB/H020314/1\t","page":"R172 - R174","date_published":"2017-03-06T00:00:00Z","doi":"10.1016/j.cub.2017.01.060","issue":"5","volume":27,"date_created":"2018-12-11T11:46:58Z","year":"2017","publication_status":"published","day":"06","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"81fd4475c5a2a2c6f4313beeab215ed9","file_id":"5330","creator":"system","date_updated":"2020-07-14T12:46:38Z","file_size":2840413,"date_created":"2018-12-12T10:18:11Z","file_name":"IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf"}],"publication":"Current Biology"},{"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2017","publication":"Discrete & Computational Geometry","day":"09","page":"871 - 888","date_created":"2018-12-11T11:47:01Z","date_published":"2017-06-09T00:00:00Z","doi":"10.1007/s00454-017-9900-0","citation":{"ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 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.","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.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1602.07907"]},"article_processing_charge":"No","publist_id":"7283","author":[{"first_name":"Benjamin","last_name":"Burton","full_name":"Burton, Benjamin"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N","full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"title":"Finding non-orientable surfaces in 3-Manifolds","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07907"}],"scopus_import":1,"intvolume":" 58","month":"06","publication_status":"published","publication_identifier":{"issn":["01795376"]},"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1379","status":"public","relation":"earlier_version"}]},"issue":"4","volume":58,"_id":"534","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-21T17:01:34Z","department":[{"_id":"UlWa"}]},{"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2018-12-11T11:47:02Z","doi":"10.1002/ange.201611998","date_published":"2017-05-20T00:00:00Z","page":"4679 - 4682","publication":"Angewandte Chemie","day":"20","year":"2017","has_accepted_license":"1","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","publist_id":"7279","author":[{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Manuela","full_name":"Stadler, Manuela","last_name":"Stadler"},{"first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"Distel, Martin","last_name":"Distel","first_name":"Martin"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","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."},"intvolume":" 129","month":"05","oa_version":"Published Version","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. "}],"ec_funded":1,"volume":129,"issue":"16","language":[{"iso":"eng"}],"file":[{"file_id":"5007","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","date_created":"2018-12-12T10:13:24Z","file_size":1668557,"date_updated":"2020-07-14T12:46:39Z","creator":"system"}],"publication_status":"published","pubrep_id":"932","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":"538","file_date_updated":"2020-07-14T12:46:39Z","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"ddc":["571"],"date_updated":"2021-01-12T08:01:33Z"},{"date_updated":"2021-01-12T08:01:48Z","ddc":["576","616"],"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:46:44Z","_id":"540","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","pubrep_id":"931","status":"public","publication_status":"published","publication_identifier":{"issn":["15537366"]},"language":[{"iso":"eng"}],"file":[{"file_id":"4944","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:26Z","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","creator":"system","date_updated":"2020-07-14T12:46:44Z","file_size":4106772}],"issue":"12","volume":13,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 13","month":"12","citation":{"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.","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.","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).","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7276","author":[{"full_name":"Khamina, Kseniya","last_name":"Khamina","first_name":"Kseniya"},{"full_name":"Lercher, Alexander","last_name":"Lercher","first_name":"Alexander"},{"first_name":"Michael","last_name":"Caldera","full_name":"Caldera, Michael"},{"last_name":"Schliehe","full_name":"Schliehe, Christopher","first_name":"Christopher"},{"last_name":"Vilagos","full_name":"Vilagos, Bojan","first_name":"Bojan"},{"last_name":"Sahin","full_name":"Sahin, Mehmet","first_name":"Mehmet"},{"last_name":"Kosack","full_name":"Kosack, Lindsay","first_name":"Lindsay"},{"first_name":"Anannya","full_name":"Bhattacharya, Anannya","last_name":"Bhattacharya"},{"last_name":"Májek","full_name":"Májek, Peter","first_name":"Peter"},{"first_name":"Alexey","full_name":"Stukalov, Alexey","last_name":"Stukalov"},{"first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","last_name":"Sacco","full_name":"Sacco, Roberto"},{"first_name":"Leo","last_name":"James","full_name":"James, Leo"},{"first_name":"Daniel","full_name":"Pinschewer, Daniel","last_name":"Pinschewer"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"first_name":"Andreas","last_name":"Bergthaler","full_name":"Bergthaler, Andreas"}],"title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","article_number":"e1006758","year":"2017","has_accepted_license":"1","publication":"PLoS Pathogens","day":"01","date_created":"2018-12-11T11:47:03Z","doi":"10.1371/journal.ppat.1006758","date_published":"2017-12-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Public Library of Science"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"article_number":"15","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Křetínská","full_name":"Křetínská, Zuzana","first_name":"Zuzana"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"}],"publist_id":"7355","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","citation":{"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","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","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.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"International Federation of Computational Logic","date_created":"2018-12-11T11:46:38Z","doi":"10.23638/LMCS-13(2:15)2017","date_published":"2017-07-03T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Logical Methods in Computer Science","day":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"journal_article","pubrep_id":"957","status":"public","_id":"466","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:33Z","date_updated":"2023-02-23T12:26:16Z","ddc":["004"],"scopus_import":1,"intvolume":" 13","month":"07","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nd/4.0/","ec_funded":1,"issue":"2","volume":13,"related_material":{"record":[{"relation":"earlier_version","id":"1657","status":"public"},{"id":"5429","status":"public","relation":"earlier_version"},{"id":"5435","status":"public","relation":"earlier_version"}]},"publication_status":"published","publication_identifier":{"issn":["18605974"]},"language":[{"iso":"eng"}],"file":[{"file_size":511832,"date_updated":"2020-07-14T12:46:33Z","creator":"system","file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","date_created":"2018-12-12T10:18:32Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"bfa405385ec6229ad5ead89ab5751639","file_id":"5354"}]},{"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-02-23T12:26:19Z","status":"public","type":"journal_article","_id":"467","related_material":{"record":[{"relation":"earlier_version","id":"1656","status":"public"},{"relation":"earlier_version","status":"public","id":"5415"},{"status":"public","id":"5436","relation":"earlier_version"}]},"issue":"4","volume":18,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15293785"]},"publication_status":"published","month":"12","intvolume":" 18","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.03598"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"title":"Nested weighted automata","publist_id":"7354","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1606.03598"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","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.","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","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017."},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"article_number":"31","doi":"10.1145/3152769","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:46:38Z","day":"01","publication":"ACM Transactions on Computational Logic (TOCL)","year":"2017","quality_controlled":"1","publisher":"ACM","oa":1},{"abstract":[{"lang":"eng","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. "}],"oa_version":"Published Version","scopus_import":1,"month":"09","intvolume":" 13","publication_identifier":{"issn":["18605974"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"08041379ba408d40664f449eb5907a8f","file_id":"5090","date_updated":"2020-07-14T12:46:33Z","file_size":279071,"creator":"system","date_created":"2018-12-12T10:14:37Z","file_name":"IST-2015-321-v1+1_main.pdf"},{"file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","date_created":"2018-12-12T10:14:38Z","creator":"system","file_size":279071,"date_updated":"2020-07-14T12:46:33Z","file_id":"5091","checksum":"08041379ba408d40664f449eb5907a8f","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":13,"related_material":{"record":[{"id":"1610","status":"public","relation":"earlier_version"},{"status":"public","id":"5438","relation":"earlier_version"}]},"issue":"3","ec_funded":1,"_id":"465","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"status":"public","pubrep_id":"955","date_updated":"2023-02-23T12:26:25Z","ddc":["004"],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:33Z","publisher":"International Federation of Computational Logic","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2017","day":"13","publication":"Logical Methods in Computer Science","date_published":"2017-09-13T00:00:00Z","doi":"10.23638/LMCS-13(3:23)2017","date_created":"2018-12-11T11:46:37Z","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"citation":{"ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/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.","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.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"publist_id":"7356","title":"Edit distance for pushdown automata"},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"doi":"10.1038/s41598-017-00107-w","date_published":"2017-03-06T00:00:00Z","date_created":"2018-12-11T11:46:53Z","has_accepted_license":"1","year":"2017","day":"06","publication":"Scientific Reports","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"article_number":"82","author":[{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publist_id":"7307","article_processing_charge":"No","title":"Amplification on undirected population structures: Comets beat stars","citation":{"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","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","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 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.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"03","intvolume":" 7","abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. 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. "}],"oa_version":"Published Version","volume":7,"related_material":{"record":[{"id":"5449","status":"public","relation":"earlier_version"}]},"issue":"1","ec_funded":1,"publication_identifier":{"issn":["20452322"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7d05cbdd914e194a019c0f91fb64e9a8","file_id":"5357","creator":"system","file_size":1536783,"date_updated":"2020-07-14T12:46:36Z","file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","date_created":"2018-12-12T10:18:35Z"}],"language":[{"iso":"eng"}],"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":"938","_id":"512","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T12:26:57Z","ddc":["004"]},{"publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","date_published":"2017-12-27T00:00:00Z","doi":"10.1145/3158118","date_created":"2021-12-05T23:01:48Z","has_accepted_license":"1","year":"2017","day":"27","publication":"Proceedings of the ACM on Programming Languages","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"article_number":"30","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Choudhary, Bhavya","last_name":"Choudhary","first_name":"Bhavya"},{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1910.00241"]},"title":"Optimal Dyck reachability for data-dependence and Alias analysis","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","month":"12","intvolume":" 2","abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks."}],"oa_version":"Published Version","issue":"POPL","related_material":{"record":[{"status":"public","id":"5455","relation":"earlier_version"}]},"volume":2,"ec_funded":1,"publication_identifier":{"eissn":["2475-1421"]},"publication_status":"published","file":[{"date_created":"2021-12-07T08:06:28Z","file_name":"2017_ACMProgLang_Chatterjee.pdf","creator":"cchlebak","date_updated":"2021-12-07T08:06:28Z","file_size":460188,"file_id":"10421","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"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)"},"conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages"},"status":"public","_id":"10416","file_date_updated":"2021-12-07T08:06:28Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T12:27:13Z","ddc":["000"]},{"related_material":{"record":[{"relation":"later_version","id":"10416","status":"public"}]},"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-870-v1+1_main.pdf","date_created":"2018-12-12T11:54:02Z","creator":"system","file_size":960491,"date_updated":"2020-07-14T12:46:59Z","checksum":"177a84a46e3ac17e87b31534ad16a4c9","file_id":"5524","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"alternative_title":["IST Austria Technical Report"],"month":"10","abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks."}],"oa_version":"Published Version","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:59Z","date_updated":"2023-02-21T15:54:10Z","ddc":["000"],"type":"technical_report","pubrep_id":"870","status":"public","_id":"5455","page":"37","date_created":"2018-12-12T11:39:26Z","date_published":"2017-10-23T00:00:00Z","doi":"10.15479/AT:IST-2017-870-v1-1","year":"2017","has_accepted_license":"1","day":"23","oa":1,"publisher":"IST Austria","article_processing_charge":"No","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Bhavya","full_name":"Choudhary, Bhavya","last_name":"Choudhary"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"title":"Optimal Dyck reachability for data-dependence and alias analysis","citation":{"chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1.","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"year":"2017","file":[{"date_updated":"2020-07-14T12:46:59Z","file_size":3460985,"creator":"system","date_created":"2018-12-12T11:53:22Z","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6321792dcfa82bf490f17615a9b22355","file_id":"5483"}],"day":"26","publication_date":"2017-06-26","date_published":"2017-06-26T00:00:00Z","date_created":"2018-12-12T11:39:24Z","abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"publisher":"IST Austria","oa":1,"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/724.","open_access":"1"}],"month":"06","date_updated":"2020-07-14T23:05:03Z","citation":{"chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017.","ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017.","apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria."},"extern":0,"author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Petritsch","orcid":"0000-0003-2724-4614","full_name":"Barbara Petritsch"}],"title":"Implementing the institutional data repository IST DataRep","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:46:59Z","_id":"5450","type":"report","status":"public","pubrep_id":"724"},{"_id":"10417","status":"public","article_type":"original","type":"journal_article","conference":{"location":"Los Angeles, CA, United States","end_date":"2018-01-13","start_date":"2018-01-07","name":"POPL: Programming Languages"},"date_updated":"2023-02-23T12:27:16Z","department":[{"_id":"KrCh"}],"oa_version":"Published Version","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.","lang":"eng"}],"month":"12","intvolume":" 2","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158119"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-1421"]},"publication_status":"published","volume":2,"issue":"POPL","related_material":{"record":[{"status":"public","id":"5448","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5456"}]},"ec_funded":1,"article_number":"31","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119."},"title":"Data-centric dynamic partial order reduction","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"first_name":"Nishant","last_name":"Sinha","full_name":"Sinha, Nishant"},{"first_name":"Kapil","last_name":"Vaidya","full_name":"Vaidya, Kapil"}],"external_id":{"arxiv":["1610.01188"]},"article_processing_charge":"No","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"day":"27","publication":"Proceedings of the ACM on Programming Languages","year":"2017","date_published":"2017-12-27T00:00:00Z","doi":"10.1145/3158119","date_created":"2021-12-05T23:01:49Z"}]