[{"file":[{"access_level":"open_access","file_name":"2020_Nonlinearity_Fischer.pdf","creator":"cziletti","file_size":1223899,"content_type":"application/pdf","file_id":"8710","relation":"main_file","success":1,"checksum":"ed90bc6eb5f32ee6157fef7f3aabc057","date_updated":"2020-10-27T12:09:57Z","date_created":"2020-10-27T12:09:57Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8697","intvolume":" 33","title":"Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model","ddc":["510"],"status":"public","issue":"11","abstract":[{"text":"In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.","lang":"eng"}],"type":"journal_article","date_published":"2020-11-01T00:00:00Z","citation":{"mla":"Fischer, Julian L., and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity, vol. 33, no. 11, IOP Publishing, 2020, pp. 5733–72, doi:10.1088/1361-6544/ab9728.","short":"J.L. Fischer, M. Kniely, Nonlinearity 33 (2020) 5733–5772.","chicago":"Fischer, Julian L, and Michael Kniely. “Variance Reduction for Effective Energies of Random Lattices in the Thomas-Fermi-von Weizsäcker Model.” Nonlinearity. IOP Publishing, 2020. https://doi.org/10.1088/1361-6544/ab9728.","ama":"Fischer JL, Kniely M. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 2020;33(11):5733-5772. doi:10.1088/1361-6544/ab9728","ista":"Fischer JL, Kniely M. 2020. Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. 33(11), 5733–5772.","apa":"Fischer, J. L., & Kniely, M. (2020). Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/ab9728","ieee":"J. L. Fischer and M. Kniely, “Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model,” Nonlinearity, vol. 33, no. 11. IOP Publishing, pp. 5733–5772, 2020."},"publication":"Nonlinearity","page":"5733-5772","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L"},{"full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","first_name":"Michael"}],"volume":33,"date_created":"2020-10-25T23:01:16Z","date_updated":"2023-08-22T10:38:38Z","year":"2020","publisher":"IOP Publishing","department":[{"_id":"JuFi"}],"publication_status":"published","file_date_updated":"2020-10-27T12:09:57Z","license":"https://creativecommons.org/licenses/by/3.0/","doi":"10.1088/1361-6544/ab9728","language":[{"iso":"eng"}],"external_id":{"isi":["000576492700001"],"arxiv":["1906.12245"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"month":"11"},{"keyword":["Multidisciplinary"],"scopus_import":"1","day":"02","article_processing_charge":"No","article_type":"original","page":"113-116","publication":"Science","citation":{"ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637."},"date_published":"2020-10-02T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning."}],"issue":"6512","title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","status":"public","intvolume":" 370","_id":"8680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"10","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"external_id":{"isi":["000579169000053"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/803635v1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/science.aba6637","ec_funded":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"American Association for the Advancement of Science","acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","year":"2020","date_created":"2020-10-19T14:09:38Z","date_updated":"2023-08-22T10:36:35Z","volume":370,"author":[{"full_name":"Tsai, Tony Y.-C.","last_name":"Tsai","first_name":"Tony Y.-C."},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xia","first_name":"Peng","full_name":"Xia, Peng"},{"full_name":"Colak-Champollion, Tugba","first_name":"Tugba","last_name":"Colak-Champollion"},{"full_name":"Knaut, Holger","last_name":"Knaut","first_name":"Holger"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Megason, Sean G.","first_name":"Sean G.","last_name":"Megason"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/sticking-together/","relation":"press_release","description":"News on IST Homepage"}]}},{"publication":"Journal of Mathematical Physics","citation":{"ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787.","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787."},"article_type":"original","date_published":"2020-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8670","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","status":"public","intvolume":" 61","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]."}],"issue":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.06644"}],"external_id":{"arxiv":["2007.06644"],"isi":["000578529200001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1063/5.0022787","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["00222488"]},"acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","year":"2020","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"JaMa"}],"author":[{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","last_name":"Zhang","first_name":"Haonan","full_name":"Zhang, Haonan"}],"date_updated":"2023-08-22T10:32:29Z","date_created":"2020-10-18T22:01:36Z","volume":61,"article_number":"102201","ec_funded":1},{"month":"10","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"doi":"10.1073/pnas.1912804117","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["32948691"],"isi":["000579045200012"]},"isi":1,"quality_controlled":"1","file_date_updated":"2020-10-27T14:57:50Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"first_name":"Ori","last_name":"Maoz","full_name":"Maoz, Ori"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"last_name":"Esteki","first_name":"Mohamad Saleh","full_name":"Esteki, Mohamad Saleh"},{"last_name":"Kiani","first_name":"Roozbeh","full_name":"Kiani, Roozbeh"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"}],"date_created":"2020-10-25T23:01:16Z","date_updated":"2023-08-22T12:11:23Z","volume":117,"acknowledgement":"We thank Udi Karpas, Roy Harpaz, Tal Tamir, Adam Haber, and Amir Bar for discussions and suggestions; and especially Oren Forkosh and Walter Senn for invaluable discussions of the learning rule. This work was supported by European Research Council Grant 311238 (to E.S.) and Israel Science Foundation Grant 1629/12 (to E.S.); as well as research support from Martin Kushner Schnur and Mr. and Mrs. Lawrence Feis (E.S.); National Institute of Mental Health Grant R01MH109180 (to R.K.); a Pew Scholarship in Biomedical Sciences (to R.K.); Simons Collaboration on the Global Brain Grant 542997 (to R.K. and E.S.); and a CRCNS (Collaborative Research in Computational Neuroscience) grant (to R.K. and E.S.).","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","day":"06","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2020-10-06T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"apa":"Maoz, O., Tkačik, G., Esteki, M. S., Kiani, R., & Schneidman, E. (2020). Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1912804117","ieee":"O. Maoz, G. Tkačik, M. S. Esteki, R. Kiani, and E. Schneidman, “Learning probabilistic neural representations with randomly connected circuits,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 25066–25073, 2020.","ista":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. 2020. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 25066–25073.","ama":"Maoz O, Tkačik G, Esteki MS, Kiani R, Schneidman E. Learning probabilistic neural representations with randomly connected circuits. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):25066-25073. doi:10.1073/pnas.1912804117","chicago":"Maoz, Ori, Gašper Tkačik, Mohamad Saleh Esteki, Roozbeh Kiani, and Elad Schneidman. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1912804117.","short":"O. Maoz, G. Tkačik, M.S. Esteki, R. Kiani, E. Schneidman, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 25066–25073.","mla":"Maoz, Ori, et al. “Learning Probabilistic Neural Representations with Randomly Connected Circuits.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 25066–73, doi:10.1073/pnas.1912804117."},"article_type":"original","page":"25066-25073","abstract":[{"text":"The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.","lang":"eng"}],"issue":"40","type":"journal_article","file":[{"creator":"cziletti","content_type":"application/pdf","file_size":1755359,"file_name":"2020_PNAS_Maoz.pdf","access_level":"open_access","date_created":"2020-10-27T14:57:50Z","date_updated":"2020-10-27T14:57:50Z","success":1,"checksum":"c6a24fdecf3f28faf447078e7a274a88","file_id":"8713","relation":"main_file"}],"oa_version":"Published Version","_id":"8698","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Learning probabilistic neural representations with randomly connected circuits","intvolume":" 117"},{"abstract":[{"lang":"eng","text":"Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E."}],"type":"conference","alternative_title":["ICRA"],"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8733","checksum":"fccf7b986ac78046918a298cc6849a50","success":1,"date_updated":"2020-11-06T10:58:49Z","date_created":"2020-11-06T10:58:49Z","access_level":"open_access","file_name":"2020_ICRA_Lechner.pdf","file_size":1070010,"content_type":"application/pdf","creator":"dernst"}],"_id":"8704","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme","ddc":["000"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2020-05-01T00:00:00Z","citation":{"ista":"Lechner M, Hasani R, Rus D, Grosu R. 2020. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, , 5446–5452.","apa":"Lechner, M., Hasani, R., Rus, D., & Grosu, R. (2020). Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In Proceedings - IEEE International Conference on Robotics and Automation (pp. 5446–5452). Paris, France: IEEE. https://doi.org/10.1109/ICRA40945.2020.9196608","ieee":"M. Lechner, R. Hasani, D. Rus, and R. Grosu, “Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme,” in Proceedings - IEEE International Conference on Robotics and Automation, Paris, France, 2020, pp. 5446–5452.","ama":"Lechner M, Hasani R, Rus D, Grosu R. Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme. In: Proceedings - IEEE International Conference on Robotics and Automation. IEEE; 2020:5446-5452. doi:10.1109/ICRA40945.2020.9196608","chicago":"Lechner, Mathias, Ramin Hasani, Daniela Rus, and Radu Grosu. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” In Proceedings - IEEE International Conference on Robotics and Automation, 5446–52. IEEE, 2020. https://doi.org/10.1109/ICRA40945.2020.9196608.","mla":"Lechner, Mathias, et al. “Gershgorin Loss Stabilizes the Recurrent Neural Network Compartment of an End-to-End Robot Learning Scheme.” Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–52, doi:10.1109/ICRA40945.2020.9196608.","short":"M. Lechner, R. Hasani, D. Rus, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2020, pp. 5446–5452."},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","page":"5446-5452","file_date_updated":"2020-11-06T10:58:49Z","author":[{"full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ramin","last_name":"Hasani","full_name":"Hasani, Ramin"},{"full_name":"Rus, Daniela","first_name":"Daniela","last_name":"Rus"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"date_updated":"2023-08-22T10:40:15Z","date_created":"2020-10-25T23:01:19Z","acknowledgement":"M.L. is supported in parts by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). R.H., and R.G. are partially supported by the Horizon-2020 ECSELProject grant No. 783163 (iDev40), and the Austrian Research Promotion Agency (FFG), Project No. 860424. R.H. and D.R. is partially supported by the Boeing Company.","year":"2020","department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","publication_identifier":{"isbn":["9781728173955"],"issn":["10504729"]},"month":"05","doi":"10.1109/ICRA40945.2020.9196608","conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2020-08-31","start_date":"2020-05-31","location":"Paris, France"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000712319503110"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1"},{"date_created":"2023-08-21T10:10:41Z","date_updated":"2023-08-22T11:03:00Z","oa_version":"Preprint","author":[{"full_name":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith","last_name":"Jamie A. P. Law-Smith","first_name":"Jamie A. P. Law-Smith"},{"full_name":"Everson, Rosa Wallace","first_name":"Rosa Wallace","last_name":"Everson"},{"full_name":"Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz","first_name":"Enrico Ramirez-Ruiz","last_name":"Enrico Ramirez-Ruiz"},{"last_name":"Mink","first_name":"Selma E. de","full_name":"Mink, Selma E. de"},{"full_name":"Son, Lieke A. C. van","last_name":"Son","first_name":"Lieke A. C. van"},{"full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"last_name":"Zellmann","first_name":"Stefan","full_name":"Zellmann, Stefan"},{"last_name":"Alejandro Vigna-Gómez","first_name":"Alejandro Vigna-Gómez","full_name":"Alejandro Vigna-Gómez, Alejandro Vigna-Gómez"},{"full_name":"Renzo, Mathieu","last_name":"Renzo","first_name":"Mathieu"},{"first_name":"Samantha","last_name":"Wu","full_name":"Wu, Samantha"},{"first_name":"Sophie L.","last_name":"Schrøder","full_name":"Schrøder, Sophie L."},{"full_name":"Foley, Ryan J.","last_name":"Foley","first_name":"Ryan J."},{"full_name":"Tenley Hutchinson-Smith, Tenley Hutchinson-Smith","first_name":"Tenley Hutchinson-Smith","last_name":"Tenley Hutchinson-Smith"}],"publication_status":"submitted","title":"Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics","status":"public","_id":"14096","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","abstract":[{"lang":"eng","text":"A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources."}],"article_number":"2011.06630","type":"preprint","language":[{"iso":"eng"}],"date_published":"2020-11-12T00:00:00Z","doi":"10.48550/arXiv.2011.06630","publication":"arXiv","citation":{"ista":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, Mink SE de, Son LAC van, Götberg YLL, Zellmann S, Alejandro Vigna-Gómez AV-G, Renzo M, Wu S, Schrøder SL, Foley RJ, Tenley Hutchinson-Smith TH-S. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv, 2011.06630.","apa":"Jamie A. P. Law-Smith, J. A. P. L.-S., Everson, R. W., Enrico Ramirez-Ruiz, E. R.-R., Mink, S. E. de, Son, L. A. C. van, Götberg, Y. L. L., … Tenley Hutchinson-Smith, T. H.-S. (n.d.). Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. https://doi.org/10.48550/arXiv.2011.06630","ieee":"J. A. P. L.-S. Jamie A. P. Law-Smith et al., “Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics,” arXiv. .","ama":"Jamie A. P. Law-Smith JAPL-S, Everson RW, Enrico Ramirez-Ruiz ER-R, et al. Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics. arXiv. doi:10.48550/arXiv.2011.06630","chicago":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, Rosa Wallace Everson, Enrico Ramirez-Ruiz Enrico Ramirez-Ruiz, Selma E. de Mink, Lieke A. C. van Son, Ylva Louise Linsdotter Götberg, Stefan Zellmann, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2011.06630.","mla":"Jamie A. P. Law-Smith, Jamie A. P. Law-Smith, et al. “Successful Common Envelope Ejection and Binary Neutron Star Formation in 3D Hydrodynamics.” ArXiv, 2011.06630, doi:10.48550/arXiv.2011.06630.","short":"J.A.P.L.-S. Jamie A. P. Law-Smith, R.W. Everson, E.R.-R. Enrico Ramirez-Ruiz, S.E. de Mink, L.A.C. van Son, Y.L.L. Götberg, S. Zellmann, A.V.-G. Alejandro Vigna-Gómez, M. Renzo, S. Wu, S.L. Schrøder, R.J. Foley, T.H.-S. Tenley Hutchinson-Smith, ArXiv (n.d.)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2011.06630"}],"external_id":{"arxiv":["2011.06630"]},"oa":1,"month":"11","day":"12","article_processing_charge":"No"},{"volume":117,"date_created":"2020-10-25T23:01:17Z","date_updated":"2023-08-22T12:11:52Z","author":[{"last_name":"Paris","first_name":"Eugenio","full_name":"Paris, Eugenio"},{"last_name":"Tseng","first_name":"Yi","full_name":"Tseng, Yi"},{"full_name":"Paerschke, Ekaterina","id":"8275014E-6063-11E9-9B7F-6338E6697425","orcid":"0000-0003-0853-8182","first_name":"Ekaterina","last_name":"Paerschke"},{"full_name":"Zhang, Wenliang","first_name":"Wenliang","last_name":"Zhang"},{"first_name":"Mary H","last_name":"Upton","full_name":"Upton, Mary H"},{"full_name":"Efimenko, Anna","first_name":"Anna","last_name":"Efimenko"},{"full_name":"Rolfs, Katharina","first_name":"Katharina","last_name":"Rolfs"},{"last_name":"McNally","first_name":"Daniel E","full_name":"McNally, Daniel E"},{"full_name":"Maurel, Laura","first_name":"Laura","last_name":"Maurel"},{"first_name":"Muntaser","last_name":"Naamneh","full_name":"Naamneh, Muntaser"},{"last_name":"Caputo","first_name":"Marco","full_name":"Caputo, Marco"},{"full_name":"Strocov, Vladimir N","last_name":"Strocov","first_name":"Vladimir N"},{"full_name":"Wang, Zhiming","first_name":"Zhiming","last_name":"Wang"},{"last_name":"Casa","first_name":"Diego","full_name":"Casa, Diego"},{"last_name":"Schneider","first_name":"Christof W","full_name":"Schneider, Christof W"},{"first_name":"Ekaterina","last_name":"Pomjakushina","full_name":"Pomjakushina, Ekaterina"},{"last_name":"Wohlfeld","first_name":"Krzysztof","full_name":"Wohlfeld, Krzysztof"},{"full_name":"Radovic, Milan","first_name":"Milan","last_name":"Radovic"},{"full_name":"Schmitt, Thorsten","last_name":"Schmitt","first_name":"Thorsten"}],"department":[{"_id":"MiLe"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"acknowledgement":"We gratefully acknowledge C. Sahle for experimental support at the ID20 beamline of the ESRF. The soft X-ray experiments were carried out at the ADRESS beamline of the Swiss Light Source, Paul Scherrer Institut (PSI). E. Paris and T.S. thank X. Lu and C. Monney for valuable discussions. The work at PSI is supported by the Swiss National Science Foundation (SNSF) through Project 200021_178867, the NCCR (National Centre of Competence in Research) MARVEL (Materials’ Revolution: Computational Design and Discovery of Novel Materials) and the Sinergia network Mott Physics Beyond the Heisenberg Model (MPBH) (SNSF Research Grants CRSII2_160765/1 and CRSII2_141962). K.W. acknowledges support by the Narodowe Centrum Nauki Projects 2016/22/E/ST3/00560 and 2016/23/B/ST3/00839. E.M.P. and M.N. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreements 754411 and 701647, respectively. M.R. was supported by the Swiss National Science Foundation under Project 200021 – 182695. This research used resources of the APS, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357.","year":"2020","ec_funded":1,"file_date_updated":"2020-10-28T11:53:12Z","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2012043117","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"arxiv":["2009.12262"],"isi":["000579059100029"],"pmid":["32958669"]},"oa":1,"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"10","file":[{"success":1,"checksum":"1638fa36b442e2868576c6dd7d6dc505","date_created":"2020-10-28T11:53:12Z","date_updated":"2020-10-28T11:53:12Z","file_id":"8715","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":1176522,"access_level":"open_access","file_name":"2020_PNAS_Paris.pdf"}],"oa_version":"Published Version","intvolume":" 117","ddc":["530"],"status":"public","title":"Strain engineering of the charge and spin-orbital interactions in Sr2IrO4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8699","issue":"40","abstract":[{"lang":"eng","text":"In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling."}],"type":"journal_article","date_published":"2020-10-06T00:00:00Z","page":"24764-24770","article_type":"original","citation":{"mla":"Paris, Eugenio, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40, National Academy of Sciences, 2020, pp. 24764–70, doi:10.1073/pnas.2012043117.","short":"E. Paris, Y. Tseng, E. Paerschke, W. Zhang, M.H. Upton, A. Efimenko, K. Rolfs, D.E. McNally, L. Maurel, M. Naamneh, M. Caputo, V.N. Strocov, Z. Wang, D. Casa, C.W. Schneider, E. Pomjakushina, K. Wohlfeld, M. Radovic, T. Schmitt, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 24764–24770.","chicago":"Paris, Eugenio, Yi Tseng, Ekaterina Paerschke, Wenliang Zhang, Mary H Upton, Anna Efimenko, Katharina Rolfs, et al. “Strain Engineering of the Charge and Spin-Orbital Interactions in Sr2IrO4.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2012043117.","ama":"Paris E, Tseng Y, Paerschke E, et al. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(40):24764-24770. doi:10.1073/pnas.2012043117","ista":"Paris E, Tseng Y, Paerschke E, Zhang W, Upton MH, Efimenko A, Rolfs K, McNally DE, Maurel L, Naamneh M, Caputo M, Strocov VN, Wang Z, Casa D, Schneider CW, Pomjakushina E, Wohlfeld K, Radovic M, Schmitt T. 2020. Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. 117(40), 24764–24770.","apa":"Paris, E., Tseng, Y., Paerschke, E., Zhang, W., Upton, M. H., Efimenko, A., … Schmitt, T. (2020). Strain engineering of the charge and spin-orbital interactions in Sr2IrO4. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2012043117","ieee":"E. Paris et al., “Strain engineering of the charge and spin-orbital interactions in Sr2IrO4,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 40. National Academy of Sciences, pp. 24764–24770, 2020."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"30","article_type":"original","citation":{"ieee":"D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” Science, vol. 370, no. 6516. American Association for the Advancement of Science, 2020.","apa":"Kampjut, D., & Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.abc4209","ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209.","ama":"Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. Science. 2020;370(6516). doi:10.1126/science.abc4209","chicago":"Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.abc4209.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020).","mla":"Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” Science, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:10.1126/science.abc4209."},"publication":"Science","date_published":"2020-10-30T00:00:00Z","type":"journal_article","issue":"6516","abstract":[{"text":"Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.","lang":"eng"}],"intvolume":" 370","title":"The coupling mechanism of mammalian respiratory complex I","ddc":["572"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8737","file":[{"checksum":"658ba90979ca9528a2efdfac8547047a","success":1,"date_created":"2020-11-26T18:47:58Z","date_updated":"2020-11-26T18:47:58Z","relation":"main_file","file_id":"8820","file_size":7618987,"content_type":"application/pdf","creator":"lsazanov","access_level":"open_access","file_name":"Full_manuscript_with_SI_opt_red.pdf"}],"oa_version":"Submitted Version","publication_identifier":{"eissn":["10959203"]},"month":"10","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000583031800004"],"pmid":["32972993"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"doi":"10.1126/science.abc4209","article_number":"eabc4209","ec_funded":1,"file_date_updated":"2020-11-26T18:47:58Z","publisher":"American Association for the Advancement of Science","department":[{"_id":"LeSa"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385","volume":370,"date_updated":"2023-08-22T12:35:38Z","date_created":"2020-11-08T23:01:23Z","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}]},{"date_published":"2020-02-01T00:00:00Z","page":"45-61","citation":{"short":"S. Li, T.B.-N. Tal Ben-Nun, S.D. Girolamo, D.-A. Alistarh, T. Hoefler, in:, Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61.","mla":"Li, Shigang, et al. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 45–61, doi:10.1145/3332466.3374528.","chicago":"Li, Shigang, Tal Ben-Nun Tal Ben-Nun, Salvatore Di Girolamo, Dan-Adrian Alistarh, and Torsten Hoefler. “Taming Unbalanced Training Workloads in Deep Learning with Partial Collective Operations.” In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 45–61. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374528.","ama":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. Taming unbalanced training workloads in deep learning with partial collective operations. In: Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:45-61. doi:10.1145/3332466.3374528","ieee":"S. Li, T. B.-N. Tal Ben-Nun, S. D. Girolamo, D.-A. Alistarh, and T. Hoefler, “Taming unbalanced training workloads in deep learning with partial collective operations,” in Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 45–61.","apa":"Li, S., Tal Ben-Nun, T. B.-N., Girolamo, S. D., Alistarh, D.-A., & Hoefler, T. (2020). Taming unbalanced training workloads in deep learning with partial collective operations. In Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 45–61). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374528","ista":"Li S, Tal Ben-Nun TB-N, Girolamo SD, Alistarh D-A, Hoefler T. 2020. Taming unbalanced training workloads in deep learning with partial collective operations. Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 45–61."},"publication":"Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","article_processing_charge":"No","day":"01","oa_version":"Preprint","title":"Taming unbalanced training workloads in deep learning with partial collective operations","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8722","abstract":[{"lang":"eng","text":"Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)\r\nachieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for\r\ndecentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show\r\nthat eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy."}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1145/3332466.3374528","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2020-02-26","location":"San Diego, CA, United States","start_date":"2020-02-22"},"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.04207"}],"external_id":{"arxiv":["1908.04207"],"isi":["000564476500004"]},"month":"02","date_updated":"2023-08-22T12:13:48Z","date_created":"2020-11-05T15:25:30Z","author":[{"last_name":"Li","first_name":"Shigang","full_name":"Li, Shigang"},{"first_name":"Tal Ben-Nun","last_name":"Tal Ben-Nun","full_name":"Tal Ben-Nun, Tal Ben-Nun"},{"first_name":"Salvatore Di","last_name":"Girolamo","full_name":"Girolamo, Salvatore Di"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Hoefler","first_name":"Torsten","full_name":"Hoefler, Torsten"}],"department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","year":"2020","ec_funded":1},{"oa_version":"Published Version","file":[{"file_name":"2020_NatureComm_Schulte.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1670898,"file_id":"8745","relation":"main_file","date_updated":"2020-11-09T07:56:24Z","date_created":"2020-11-09T07:56:24Z","success":1,"checksum":"b2688f0347e69e6629bba582077278c5"}],"status":"public","ddc":["570"],"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8744","abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"type":"journal_article","date_published":"2020-11-04T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications, vol. 11, 5569, Springer Nature, 2020, doi:10.1038/s41467-020-19372-x.","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19372-x.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 2020;11. doi:10.1038/s41467-020-19372-x","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19372-x","ieee":"L. Schulte et al., “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” Nature Communications, vol. 11. Springer Nature, 2020."},"day":"04","article_processing_charge":"No","has_accepted_license":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"scopus_import":"1","date_created":"2020-11-09T07:49:36Z","date_updated":"2023-08-22T12:36:07Z","volume":11,"author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"full_name":"Mao, Jiafei","first_name":"Jiafei","last_name":"Mao"},{"full_name":"Reitz, Julian","first_name":"Julian","last_name":"Reitz"},{"first_name":"Sridhar","last_name":"Sreeramulu","full_name":"Sreeramulu, Sridhar"},{"full_name":"Kudlinzki, Denis","first_name":"Denis","last_name":"Kudlinzki"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Meier-Credo, Jakob","first_name":"Jakob","last_name":"Meier-Credo"},{"first_name":"Krishna","last_name":"Saxena","full_name":"Saxena, Krishna"},{"last_name":"Buhr","first_name":"Florian","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","last_name":"Langer","first_name":"Julian D."},{"last_name":"Blackledge","first_name":"Martin","full_name":"Blackledge, Martin"},{"full_name":"Frangakis, Achilleas S.","last_name":"Frangakis","first_name":"Achilleas S."},{"last_name":"Glaubitz","first_name":"Clemens","full_name":"Glaubitz, Clemens"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"year":"2020","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","file_date_updated":"2020-11-09T07:56:24Z","article_number":"5569","language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19372-x","isi":1,"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"},"external_id":{"isi":["000592028600001"]},"oa":1,"month":"11","publication_identifier":{"issn":["2041-1723"]}},{"article_processing_charge":"No","month":"01","day":"18","citation":{"chicago":"Gaudi, B. Scott, Sara Seager, Bertrand Mennesson, Alina Kiessling, Keith Warfield, Kerri Cahoy, John T. Clarke, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2001.06683.","short":"B.S. Gaudi, S. Seager, B. Mennesson, A. Kiessling, K. Warfield, K. Cahoy, J.T. Clarke, S.D.-G. Shawn Domagal-Goldman, L. Feinberg, O. Guyon, J. Kasdin, D. Mawet, P. Plavchan, T. Robinson, L. Rogers, P. Scowen, R. Somerville, K. Stapelfeldt, C. Stark, D. Stern, M. Turnbull, R. Amini, G. Kuan, S. Martin, R. Morgan, D. Redding, H.P. Stahl, R. Webb, O.A.-S. Oscar Alvarez-Salazar, W.L. Arnold, M. Arya, B. Balasubramanian, M. Baysinger, R. Bell, C. Below, J. Benson, L. Blais, J. Booth, R. Bourgeois, C. Bradford, A. Brewer, T. Brooks, E. Cady, M. Caldwell, R. Calvet, S. Carr, D. Chan, V. Cormarkovic, K. Coste, C. Cox, R. Danner, J. Davis, L. Dewell, L. Dorsett, D. Dunn, M. East, M. Effinger, R. Eng, G. Freebury, J. Garcia, J. Gaskin, S. Greene, J. Hennessy, E. Hilgemann, B. Hood, W. Holota, S. Howe, P. Huang, T. Hull, R. Hunt, K. Hurd, S. Johnson, A. Kissil, B. Knight, D. Kolenz, O. Kraus, J. Krist, M. Li, D. Lisman, M. Mandic, J. Mann, L. Marchen, C.M.-R. Colleen Marrese-Reading, J. McCready, J. McGown, J. Missun, A. Miyaguchi, B. Moore, B. Nemati, S. Nikzad, J. Nissen, M. Novicki, T. Perrine, C. Pineda, O. Polanco, D. Putnam, A. Qureshi, M. Richards, A.J.E. Riggs, M. Rodgers, M. Rud, N. Saini, D. Scalisi, D. Scharf, K. Schulz, G. Serabyn, N. Sigrist, G. Sikkia, A. Singleton, S. Shaklan, S. Smith, B. Southerd, M. Stahl, J. Steeves, B. Sturges, C. Sullivan, H. Tang, N. Taras, J. Tesch, M. Therrell, H. Tseng, M. Valente, D.V. Buren, J. Villalvazo, S. Warwick, D. Webb, T. Westerhoff, R. Wofford, G. Wu, J. Woo, M. Wood, J. Ziemer, G. Arney, J. Anderson, J.M.-A. Jesús Maíz-Apellániz, J. Bartlett, R. Belikov, E. Bendek, B. Cenko, E. Douglas, S. Dulz, C. Evans, V. Faramaz, Y.K. Feng, H. Ferguson, K. Follette, S. Ford, M. García, M. Geha, D. Gelino, Y.L.L. Götberg, S. Hildebrandt, R. Hu, K. Jahnke, G. Kennedy, L. Kreidberg, A. Isella, E. Lopez, F. Marchis, L. Macri, M. Marley, W. Matzko, J. Mazoyer, S. McCandliss, T. Meshkat, C. Mordasini, P. Morris, E. Nielsen, P. Newman, E. Petigura, M. Postman, A. Reines, A. Roberge, I. Roederer, G. Ruane, E. Schwieterman, D. Sirbu, C. Spalding, H. Teplitz, J. Tumlinson, N. Turner, J. Werk, A. Wofford, M. Wyatt, A. Young, R. Zellem, ArXiv (n.d.).","mla":"Gaudi, B. Scott, et al. “The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Final Report.” ArXiv, 2001.06683, doi:10.48550/arXiv.2001.06683.","apa":"Gaudi, B. S., Seager, S., Mennesson, B., Kiessling, A., Warfield, K., Cahoy, K., … Zellem, R. (n.d.). The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. https://doi.org/10.48550/arXiv.2001.06683","ieee":"B. S. Gaudi et al., “The habitable exoplanet observatory (HabEx) mission concept study final report,” arXiv. .","ista":"Gaudi BS et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv, 2001.06683.","ama":"Gaudi BS, Seager S, Mennesson B, et al. The habitable exoplanet observatory (HabEx) mission concept study final report. arXiv. doi:10.48550/arXiv.2001.06683"},"oa":1,"external_id":{"arxiv":["2001.06683"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2001.06683"}],"publication":"arXiv","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2001.06683","date_published":"2020-01-18T00:00:00Z","type":"preprint","article_number":"2001.06683","extern":"1","abstract":[{"text":"The Habitable Exoplanet Observatory, or HabEx, has been designed to be the Great Observatory of the 2030s. For the first time in human history, technologies have matured sufficiently to enable an affordable space-based telescope mission capable of discovering and characterizing Earthlike planets orbiting nearby bright sunlike stars in order to search for signs of habitability and biosignatures. Such a mission can also be equipped with instrumentation that will enable broad and exciting general astrophysics and planetary science not possible from current or planned facilities. HabEx is a space telescope with unique imaging and multi-object spectroscopic capabilities at wavelengths ranging from ultraviolet (UV) to near-IR. These capabilities allow for a broad suite of compelling science that cuts across the entire NASA astrophysics portfolio. HabEx has three primary science goals: (1) Seek out nearby worlds and explore their habitability; (2) Map out nearby planetary systems and understand the diversity of the worlds they contain; (3) Enable new explorations of astrophysical systems from our own solar system to external galaxies by extending our reach in the UV through near-IR. This Great Observatory science will be selected through a competed GO program, and will account for about 50% of the HabEx primary mission. The preferred HabEx architecture is a 4m, monolithic, off-axis telescope that is diffraction-limited at 0.4 microns and is in an L2 orbit. HabEx employs two starlight suppression systems: a coronagraph and a starshade, each with their own dedicated instrument.","lang":"eng"}],"publication_status":"submitted","status":"public","title":"The habitable exoplanet observatory (HabEx) mission concept study final report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14095","year":"2020","oa_version":"Preprint","date_updated":"2023-08-22T13:13:18Z","date_created":"2023-08-21T10:10:21Z","author":[{"full_name":"Gaudi, B. Scott","first_name":"B. 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Katherina"},{"full_name":"Ferguson, Harry","first_name":"Harry","last_name":"Ferguson"},{"full_name":"Follette, Kate","last_name":"Follette","first_name":"Kate"},{"full_name":"Ford, Saavik","first_name":"Saavik","last_name":"Ford"},{"first_name":"Miriam","last_name":"García","full_name":"García, Miriam"},{"first_name":"Marla","last_name":"Geha","full_name":"Geha, Marla"},{"full_name":"Gelino, Dawn","last_name":"Gelino","first_name":"Dawn"},{"full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","first_name":"Ylva Louise Linsdotter"},{"full_name":"Hildebrandt, Sergi","first_name":"Sergi","last_name":"Hildebrandt"},{"last_name":"Hu","first_name":"Renyu","full_name":"Hu, Renyu"},{"full_name":"Jahnke, Knud","first_name":"Knud","last_name":"Jahnke"},{"last_name":"Kennedy","first_name":"Grant","full_name":"Kennedy, Grant"},{"full_name":"Kreidberg, Laura","first_name":"Laura","last_name":"Kreidberg"},{"last_name":"Isella","first_name":"Andrea","full_name":"Isella, Andrea"},{"full_name":"Lopez, Eric","first_name":"Eric","last_name":"Lopez"},{"full_name":"Marchis, Franck","last_name":"Marchis","first_name":"Franck"},{"last_name":"Macri","first_name":"Lucas","full_name":"Macri, Lucas"},{"first_name":"Mark","last_name":"Marley","full_name":"Marley, Mark"},{"full_name":"Matzko, William","last_name":"Matzko","first_name":"William"},{"full_name":"Mazoyer, Johan","first_name":"Johan","last_name":"Mazoyer"},{"last_name":"McCandliss","first_name":"Stephan","full_name":"McCandliss, Stephan"},{"last_name":"Meshkat","first_name":"Tiffany","full_name":"Meshkat, Tiffany"},{"first_name":"Christoph","last_name":"Mordasini","full_name":"Mordasini, Christoph"},{"first_name":"Patrick","last_name":"Morris","full_name":"Morris, Patrick"},{"last_name":"Nielsen","first_name":"Eric","full_name":"Nielsen, Eric"},{"full_name":"Newman, Patrick","first_name":"Patrick","last_name":"Newman"},{"first_name":"Erik","last_name":"Petigura","full_name":"Petigura, Erik"},{"last_name":"Postman","first_name":"Marc","full_name":"Postman, Marc"},{"full_name":"Reines, Amy","last_name":"Reines","first_name":"Amy"},{"last_name":"Roberge","first_name":"Aki","full_name":"Roberge, Aki"},{"full_name":"Roederer, Ian","first_name":"Ian","last_name":"Roederer"},{"full_name":"Ruane, Garreth","last_name":"Ruane","first_name":"Garreth"},{"full_name":"Schwieterman, Edouard","last_name":"Schwieterman","first_name":"Edouard"},{"last_name":"Sirbu","first_name":"Dan","full_name":"Sirbu, Dan"},{"first_name":"Christopher","last_name":"Spalding","full_name":"Spalding, Christopher"},{"first_name":"Harry","last_name":"Teplitz","full_name":"Teplitz, Harry"},{"full_name":"Tumlinson, Jason","last_name":"Tumlinson","first_name":"Jason"},{"first_name":"Neal","last_name":"Turner","full_name":"Turner, Neal"},{"full_name":"Werk, Jessica","last_name":"Werk","first_name":"Jessica"},{"full_name":"Wofford, Aida","first_name":"Aida","last_name":"Wofford"},{"full_name":"Wyatt, Mark","last_name":"Wyatt","first_name":"Mark"},{"first_name":"Amber","last_name":"Young","full_name":"Young, Amber"},{"full_name":"Zellem, Rob","last_name":"Zellem","first_name":"Rob"}]},{"abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2498594,"creator":"dernst","file_name":"2020_PlosCompBio_Kaveh.pdf","access_level":"open_access","date_created":"2020-11-18T07:26:10Z","date_updated":"2020-11-18T07:26:10Z","checksum":"555456dd0e47bcf9e0994bcb95577e88","success":1,"relation":"main_file","file_id":"8768"}],"ddc":["000"],"title":"The Moran process on 2-chromatic graphs","status":"public","intvolume":" 16","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"scopus_import":"1","date_published":"2020-11-05T00:00:00Z","article_type":"original","publication":"PLOS Computational Biology","citation":{"chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402.","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402"},"file_date_updated":"2020-11-18T07:26:10Z","article_number":"e1008402","date_updated":"2023-08-22T12:49:18Z","date_created":"2020-11-18T07:20:23Z","volume":16,"author":[{"last_name":"Kaveh","first_name":"Kamran","full_name":"Kaveh, Kamran"},{"first_name":"Alex","last_name":"McAvoy","full_name":"McAvoy, Alex"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","year":"2020","acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","month":"11","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1008402","isi":1,"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,"external_id":{"isi":["000591317200004"]}},{"ec_funded":1,"article_number":"9314994","author":[{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"full_name":"Freire, Daniel","last_name":"Freire","first_name":"Daniel"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"}],"date_updated":"2023-08-22T12:48:18Z","date_created":"2020-11-10T07:04:57Z","year":"2020","publisher":"IEEE","department":[{"_id":"ToHe"}],"publication_status":"published","publication_identifier":{"isbn":["9781728191485"]},"month":"12","doi":"10.1109/MEMOCODE51338.2020.9314994","conference":{"end_date":"2020-12-04","start_date":"2020-12-02","location":"Virtual Conference","name":"MEMOCODE: Conference on Formal Methods and Models for System Design"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2006.12325"}],"external_id":{"isi":["000661920400013"],"arxiv":["2006.12325"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"8750","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2020-12-04T00:00:00Z","citation":{"ama":"Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In: 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE; 2020. doi:10.1109/MEMOCODE51338.2020.9314994","apa":"Forets, M., Freire, D., & Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. Virtual Conference: IEEE. https://doi.org/10.1109/MEMOCODE51338.2020.9314994","ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions,” in 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, Virtual Conference, 2020.","ista":"Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","mla":"Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, 9314994, IEEE, 2020, doi:10.1109/MEMOCODE51338.2020.9314994.","chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with Time-Triggered Transitions.” In 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. IEEE, 2020. https://doi.org/10.1109/MEMOCODE51338.2020.9314994."},"publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design"},{"quality_controlled":"1","isi":1,"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504"}],"external_id":{"arxiv":["2004.02831"],"isi":["000587107200002"]},"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":"10.1007/s10955-020-02663-4","month":"12","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Springer Nature","acknowledgement":"The research of A.M. was partially supported by the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center SFB 1114 Scaling Cascades in Complex Systems (Project No. 235221301), through the Subproject C05 Effective models for materials and interfaces with multiple scales. J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117), and by the Austrian Science Fund (FWF), Project SFB F65. The authors thank Christof Schütte, Robert I. A. Patterson, and Stefanie Winkelmann for helpful and stimulating discussions. Open access funding provided by Austrian Science Fund (FWF).","year":"2020","date_updated":"2023-08-22T13:24:27Z","date_created":"2020-11-15T23:01:18Z","volume":181,"author":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"},{"last_name":"Mielke","first_name":"Alexander","full_name":"Mielke, Alexander"}],"file_date_updated":"2021-02-04T10:29:11Z","ec_funded":1,"article_type":"original","page":"2257-2303","publication":"Journal of Statistical Physics","citation":{"ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 2020;181(6):2257-2303. doi:10.1007/s10955-020-02663-4","ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” Journal of Statistical Physics, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020.","apa":"Maas, J., & Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-020-02663-4","ista":"Maas J, Mielke A. 2020. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 181(6), 2257–2303.","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:10.1007/s10955-020-02663-4.","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” Journal of Statistical Physics. Springer Nature, 2020. https://doi.org/10.1007/s10955-020-02663-4."},"date_published":"2020-12-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["510"],"title":"Modeling of chemical reaction systems with detailed balance using gradient structures","intvolume":" 181","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8758","file":[{"success":1,"checksum":"bc2b63a90197b97cbc73eccada4639f5","date_updated":"2021-02-04T10:29:11Z","date_created":"2021-02-04T10:29:11Z","file_id":"9087","relation":"main_file","creator":"dernst","file_size":753596,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_JourStatPhysics_Maas.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels.","lang":"eng"}],"issue":"6"},{"type":"research_data_reference","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"publisher":"Zenodo","department":[{"_id":"JoFi"}],"ddc":["530"],"title":"Surpassing the resistance quantum with a geometric superinductor","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13070","year":"2020","oa_version":"Published Version","date_updated":"2023-08-22T13:23:57Z","date_created":"2023-05-23T16:42:30Z","related_material":{"record":[{"id":"8755","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda"},{"full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea"},{"last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"article_processing_charge":"No","month":"09","day":"27","citation":{"ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882."},"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,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4052883","open_access":"1"}],"doi":"10.5281/ZENODO.4052882","date_published":"2020-09-27T00:00:00Z"},{"article_type":"original","publication":"Nature Communications","citation":{"ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","ieee":"L. Nicolai et al., “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-19515-0","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 2020;11. doi:10.1038/s41467-020-19515-0","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-19515-0.","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” Nature Communications, vol. 11, 5778, Springer Nature, 2020, doi:10.1038/s41467-020-19515-0.","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020)."},"date_published":"2020-11-13T00:00:00Z","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","ddc":["570"],"status":"public","intvolume":" 11","_id":"8787","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"success":1,"checksum":"485b7b6cf30198ba0ce126491a28f125","date_created":"2020-11-23T13:29:49Z","date_updated":"2020-11-23T13:29:49Z","file_id":"8798","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":7035340,"access_level":"open_access","file_name":"2020_NatureComm_Nicolai.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"isi":1,"quality_controlled":"1","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"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"},"external_id":{"isi":["000594648000014"],"pmid":["33188196"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-020-19515-0","month":"11","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"year":"2020","acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","pmid":1,"date_updated":"2023-08-22T13:26:26Z","date_created":"2020-11-22T23:01:23Z","volume":11,"author":[{"last_name":"Nicolai","first_name":"Leo","full_name":"Nicolai, Leo"},{"first_name":"Karin","last_name":"Schiefelbein","full_name":"Schiefelbein, Karin"},{"last_name":"Lipsky","first_name":"Silvia","full_name":"Lipsky, Silvia"},{"first_name":"Alexander","last_name":"Leunig","full_name":"Leunig, Alexander"},{"last_name":"Hoffknecht","first_name":"Marie","full_name":"Hoffknecht, Marie"},{"last_name":"Pekayvaz","first_name":"Kami","full_name":"Pekayvaz, Kami"},{"full_name":"Raude, Ben","last_name":"Raude","first_name":"Ben"},{"last_name":"Marx","first_name":"Charlotte","full_name":"Marx, Charlotte"},{"last_name":"Ehrlich","first_name":"Andreas","full_name":"Ehrlich, Andreas"},{"first_name":"Joachim","last_name":"Pircher","full_name":"Pircher, Joachim"},{"full_name":"Zhang, Zhe","first_name":"Zhe","last_name":"Zhang"},{"full_name":"Saleh, Inas","last_name":"Saleh","first_name":"Inas"},{"full_name":"Marel, Anna-Kristina","first_name":"Anna-Kristina","last_name":"Marel"},{"last_name":"Löf","first_name":"Achim","full_name":"Löf, Achim"},{"full_name":"Petzold, Tobias","first_name":"Tobias","last_name":"Petzold"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"last_name":"Stark","first_name":"Konstantin","full_name":"Stark, Konstantin"},{"first_name":"Robert","last_name":"Pick","full_name":"Pick, Robert"},{"last_name":"Rosenberger","first_name":"Gerhild","full_name":"Rosenberger, Gerhild"},{"full_name":"Weckbach, Ludwig","first_name":"Ludwig","last_name":"Weckbach"},{"last_name":"Uhl","first_name":"Bernd","full_name":"Uhl, Bernd"},{"last_name":"Xia","first_name":"Sheng","full_name":"Xia, Sheng"},{"full_name":"Reichel, Christoph Andreas","last_name":"Reichel","first_name":"Christoph Andreas"},{"full_name":"Walzog, Barbara","first_name":"Barbara","last_name":"Walzog"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"last_name":"Bender","first_name":"Markus","full_name":"Bender, Markus"},{"full_name":"Li, Rong","first_name":"Rong","last_name":"Li"},{"last_name":"Massberg","first_name":"Steffen","full_name":"Massberg, Steffen"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"article_number":"5778","file_date_updated":"2020-11-23T13:29:49Z","ec_funded":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2020-11-04T00:00:00Z","citation":{"ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” Mathematics, vol. 8, no. 11. MDPI, 2020.","apa":"Kleshnina, M., Streipert, S., Filar, J., & Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. Mathematics. MDPI. https://doi.org/10.3390/math8111945","ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. Mathematics. 2020;8(11). doi:10.3390/math8111945","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” Mathematics. MDPI, 2020. https://doi.org/10.3390/math8111945.","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” Mathematics, vol. 8, no. 11, 1945, MDPI, 2020, doi:10.3390/math8111945.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020)."},"publication":"Mathematics","article_type":"original","issue":"11","abstract":[{"lang":"eng","text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty."}],"type":"journal_article","file":[{"success":1,"checksum":"61cfcc3b35760656ce7a9385a4ace5d2","date_created":"2020-11-23T13:06:30Z","date_updated":"2020-11-23T13:06:30Z","file_id":"8797","relation":"main_file","creator":"dernst","file_size":565191,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Mathematics_Kleshnina.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8789","intvolume":" 8","ddc":["000"],"status":"public","title":"Prioritised learning in snowdrift-type games","publication_identifier":{"eissn":["22277390"]},"month":"11","doi":"10.3390/math8111945","language":[{"iso":"eng"}],"external_id":{"isi":["000593962100001"]},"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,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-11-23T13:06:30Z","article_number":"1945","author":[{"full_name":"Kleshnina, Maria","first_name":"Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Streipert","first_name":"Sabrina","full_name":"Streipert, Sabrina"},{"full_name":"Filar, Jerzy","last_name":"Filar","first_name":"Jerzy"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"volume":8,"date_created":"2020-11-22T23:01:24Z","date_updated":"2023-08-22T13:25:45Z","year":"2020","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","department":[{"_id":"KrCh"}],"publisher":"MDPI","publication_status":"published"},{"citation":{"ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual .","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020."},"publication":"Proceedings of the International Conference on Embedded Software","date_published":"2020-01-01T00:00:00Z","keyword":["reachability","hybrid systems","decomposition"],"has_accepted_license":"1","article_processing_charge":"No","title":"Reachability analysis of linear hybrid systems via block decomposition","ddc":["000"],"status":"public","_id":"8287","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","file":[{"date_updated":"2020-08-24T12:53:15Z","date_created":"2020-08-24T12:53:15Z","success":1,"checksum":"d19e97d0f8a3a441dc078ec812297d75","file_id":"8288","relation":"main_file","creator":"cschilli","content_type":"application/pdf","file_size":696384,"file_name":"2020EMSOFT.pdf","access_level":"open_access"}],"type":"conference","abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","external_id":{"arxiv":["1905.02458"]},"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"}],"conference":{"end_date":"2020-09-25","start_date":"2020-09-20","location":"Virtual ","name":"EMSOFT: International Conference on Embedded Software"},"department":[{"_id":"ToHe"}],"publication_status":"published","year":"2020","date_created":"2020-08-24T12:56:20Z","date_updated":"2023-08-22T13:27:32Z","related_material":{"record":[{"id":"8790","relation":"later_version","status":"public"}]},"author":[{"first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"full_name":"Forets, Marcelo","last_name":"Forets","first_name":"Marcelo"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"}],"ec_funded":1,"file_date_updated":"2020-08-24T12:53:15Z"},{"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","year":"2020","publication_status":"published","publisher":"IEEE","department":[{"_id":"ToHe"}],"author":[{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"last_name":"Potomkin","first_name":"Kostiantyn","full_name":"Potomkin, Kostiantyn"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"}],"related_material":{"record":[{"id":"8287","status":"public","relation":"earlier_version"}]},"date_updated":"2023-08-22T13:27:33Z","date_created":"2020-11-22T23:01:25Z","volume":39,"ec_funded":1,"external_id":{"isi":["000587712700072"],"arxiv":["1905.02458"]},"main_file_link":[{"url":"https://arxiv.org/abs/1905.02458","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"doi":"10.1109/TCAD.2020.3012859","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["02780070"],"eissn":["19374151"]},"_id":"8790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Reachability analysis of linear hybrid systems via block decomposition","status":"public","intvolume":" 39","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"issue":"11","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","citation":{"ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 2020;39(11):4018-4029. doi:10.1109/TCAD.2020.3012859","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE. https://doi.org/10.1109/TCAD.2020.3012859","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:10.1109/TCAD.2020.3012859.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. IEEE, 2020. https://doi.org/10.1109/TCAD.2020.3012859."},"article_type":"original","page":"4018-4029","date_published":"2020-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"author":[{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"full_name":"Dadarou, Despoina","last_name":"Dadarou","first_name":"Despoina"},{"last_name":"Kargios","first_name":"Nestoras","full_name":"Kargios, Nestoras"},{"last_name":"Mallioura","first_name":"Areti","full_name":"Mallioura, Areti"},{"full_name":"Fernandez-Fuentes, Narcis","last_name":"Fernandez-Fuentes","first_name":"Narcis"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Doonan, John H.","first_name":"John H.","last_name":"Doonan"}],"date_created":"2020-12-06T23:01:14Z","date_updated":"2023-08-24T10:50:00Z","volume":11,"year":"2020","acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Frontiers","file_date_updated":"2020-12-09T09:14:19Z","article_number":"586870","doi":"10.3389/fpls.2020.586870","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"},"external_id":{"isi":["000591637000001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"eissn":["1664-462X"]},"oa_version":"Published Version","file":[{"file_id":"8929","relation":"main_file","success":1,"checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","date_updated":"2020-12-09T09:14:19Z","date_created":"2020-12-09T09:14:19Z","access_level":"open_access","file_name":"2020_Frontiers_Nibau.pdf","creator":"dernst","file_size":1833244,"content_type":"application/pdf"}],"_id":"8924","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["580"],"title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","intvolume":" 11","abstract":[{"text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression.","lang":"eng"}],"type":"journal_article","date_published":"2020-11-10T00:00:00Z","publication":"Frontiers in Plant Science","citation":{"short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science, vol. 11, 586870, Frontiers, 2020, doi:10.3389/fpls.2020.586870.","chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.586870.","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.586870","ieee":"C. Nibau et al., “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.","apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., & Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.586870","ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870."},"article_type":"original","day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"}]