[{"citation":{"ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Peixin","full_name":"Wang, Peixin","last_name":"Wang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Deng","full_name":"Deng, Yuxin","first_name":"Yuxin"},{"full_name":"Xu, Ming","last_name":"Xu","first_name":"Ming"}],"external_id":{"arxiv":["1902.04744"]},"article_processing_charge":"No","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","article_number":"25","project":[{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2020","day":"01","publication":"Proceedings of the ACM on Programming Languages","doi":"10.1145/3371093","date_published":"2020-01-01T00:00:00Z","date_created":"2020-08-30T22:01:12Z","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","quality_controlled":"1","publisher":"ACM","oa":1,"date_updated":"2024-02-22T15:16:45Z","ddc":["004"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-09-01T11:12:58Z","_id":"8324","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["2475-1421"]},"publication_status":"published","file":[{"file_id":"8328","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-01T11:12:58Z","file_name":"2019_ACM_POPL_Wang.pdf","creator":"cziletti","date_updated":"2020-09-01T11:12:58Z","file_size":564151}],"language":[{"iso":"eng"}],"issue":"POPL","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"volume":4,"abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 4"},{"quality_controlled":"1","publisher":"Karger Publishers","publication":"Brain, Behavior and Evolution","day":"01","year":"2020","isi":1,"date_created":"2019-12-09T09:04:13Z","doi":"10.1159/000504162","date_published":"2020-01-01T00:00:00Z","page":"27-36","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Salazar, Juan Esteban, et al. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution, vol. 94, no. 1–4, Karger Publishers, 2020, pp. 27–36, doi:10.1159/000504162.","ieee":"J. E. Salazar et al., “Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes),” Brain, Behavior and Evolution, vol. 94, no. 1–4. Karger Publishers, pp. 27–36, 2020.","short":"J.E. Salazar, D. Severin, T.A. Vega Zuniga, P. Fernández-Aburto, A. Deichler, M. Sallaberry A., J. Mpodozis, Brain, Behavior and Evolution 94 (2020) 27–36.","ama":"Salazar JE, Severin D, Vega Zuniga TA, et al. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 2020;94(1-4):27-36. doi:10.1159/000504162","apa":"Salazar, J. E., Severin, D., Vega Zuniga, T. A., Fernández-Aburto, P., Deichler, A., Sallaberry A., M., & Mpodozis, J. (2020). Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. Karger Publishers. https://doi.org/10.1159/000504162","chicago":"Salazar, Juan Esteban, Daniel Severin, Tomas A Vega Zuniga, Pedro Fernández-Aburto, Alfonso Deichler, Michel Sallaberry A., and Jorge Mpodozis. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution. Karger Publishers, 2020. https://doi.org/10.1159/000504162.","ista":"Salazar JE, Severin D, Vega Zuniga TA, Fernández-Aburto P, Deichler A, Sallaberry A. M, Mpodozis J. 2020. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 94(1–4), 27–36."},"title":"Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes)","external_id":{"isi":["000522856600004"],"pmid":["31751995"]},"article_processing_charge":"No","author":[{"full_name":"Salazar, Juan Esteban","last_name":"Salazar","first_name":"Juan Esteban"},{"first_name":"Daniel","full_name":"Severin, Daniel","last_name":"Severin"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fernández-Aburto","full_name":"Fernández-Aburto, Pedro","first_name":"Pedro"},{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"first_name":"Michel","full_name":"Sallaberry A., Michel","last_name":"Sallaberry A."},{"first_name":"Jorge","full_name":"Mpodozis, Jorge","last_name":"Mpodozis"}],"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Nocturnal animals that rely on their visual system for foraging, mating, and navigation usually exhibit specific traits associated with living in scotopic conditions. Most nocturnal birds have several visual specializations, such as enlarged eyes and an increased orbital convergence. However, the actual role of binocular vision in nocturnal foraging is still debated. Nightjars (Aves: Caprimulgidae) are predators that actively pursue and capture flying insects in crepuscular and nocturnal environments, mainly using a conspicuous “sit-and-wait” tactic on which pursuit begins with an insect flying over the bird that sits on the ground. In this study, we describe the visual system of the band-winged nightjar (Systellura longirostris), with emphasis on anatomical features previously described as relevant for nocturnal birds. Orbit convergence, determined by 3D scanning of the skull, was 73.28°. The visual field, determined by ophthalmoscopic reflex, exhibits an area of maximum binocular overlap of 42°, and it is dorsally oriented. The eyes showed a nocturnal-like normalized corneal aperture/axial length index. Retinal ganglion cells (RGCs) were relatively scant, and distributed in an unusual oblique-band pattern, with higher concentrations in the ventrotemporal quadrant. Together, these results indicate that the band-winged nightjar exhibits a retinal specialization associated with the binocular area of their dorsal visual field, a relevant area for pursuit triggering and prey attacks. The RGC distribution observed is unusual among birds, but similar to that of some visually dependent insectivorous bats, suggesting that those features might be convergent in relation to feeding strategies."}],"intvolume":" 94","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0006-8977"],"eissn":["1421-9743"]},"issue":"1-4","volume":94,"_id":"7160","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-02-22T15:18:34Z","department":[{"_id":"MaJö"}]},{"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"isi":1,"year":"2020","day":"01","publication":"Annals of Probability","page":"963-1001","date_published":"2020-03-01T00:00:00Z","doi":"10.1214/19-AOP1379","date_created":"2019-03-28T09:20:08Z","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379.","ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001.","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes","last_name":"Alt"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.07744"],"isi":["000528269100013"]},"title":"Correlated random matrices: Band rigidity and edge universality","abstract":[{"text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07744"}],"month":"03","intvolume":" 48","publication_identifier":{"issn":["0091-1798"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"},{"id":"6179","status":"public","relation":"dissertation_contains"}]},"volume":48,"issue":"2","ec_funded":1,"_id":"6184","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-02-22T14:34:33Z","department":[{"_id":"LaEr"}]},{"status":"public","keyword":["Plant Science","Molecular Biology"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15037","file_date_updated":"2024-02-28T12:39:56Z","department":[{"_id":"EvBe"}],"ddc":["580"],"date_updated":"2024-02-28T12:41:52Z","month":"05","intvolume":" 13","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants."}],"issue":"5","volume":13,"file":[{"success":1,"checksum":"c538a5008f7827f62d17d40a3bfabe65","file_id":"15038","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","date_created":"2024-02-28T12:39:56Z","creator":"dernst","file_size":3089212,"date_updated":"2024-02-28T12:39:56Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1674-2052"]},"publication_status":"published","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","author":[{"last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette"},{"first_name":"Maximilian","full_name":"Schwihla, Maximilian","last_name":"Schwihla"},{"last_name":"De-Araújo","full_name":"De-Araújo, Lucinda","first_name":"Lucinda"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","full_name":"Artner, Christina","last_name":"Artner"},{"last_name":"Jörg","full_name":"Jörg, Lisa","first_name":"Lisa"},{"last_name":"Konstantinova","full_name":"Konstantinova, Nataliia","first_name":"Nataliia"},{"first_name":"Christian","full_name":"Luschnig, Christian","last_name":"Luschnig"},{"last_name":"Korbei","full_name":"Korbei, Barbara","first_name":"Barbara"}],"external_id":{"pmid":["32087370"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"date_published":"2020-05-04T00:00:00Z","doi":"10.1016/j.molp.2020.02.012","date_created":"2024-02-28T08:55:56Z","page":"717-731","day":"04","publication":"Molecular Plant","has_accepted_license":"1","year":"2020"},{"citation":{"mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Higor Vinícius Dias","full_name":"Rosa, Higor Vinícius Dias","last_name":"Rosa"},{"full_name":"Leonardo, Diego Antonio","last_name":"Leonardo","first_name":"Diego Antonio"},{"full_name":"Brognara, Gabriel","last_name":"Brognara","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"first_name":"José","full_name":"Brandão-Neto, José","last_name":"Brandão-Neto"},{"last_name":"D'Muniz Pereira","full_name":"D'Muniz Pereira, Humberto","first_name":"Humberto"},{"first_name":"Ana Paula Ulian","full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo"},{"first_name":"Richard Charles","full_name":"Garratt, Richard Charles","last_name":"Garratt"}],"external_id":{"pmid":["32910969"]},"article_processing_charge":"No","title":"Molecular recognition at septin interfaces: The switches hold the key","year":"2020","day":"02","publication":"Journal of Molecular Biology","page":"5784-5801","doi":"10.1016/j.jmb.2020.09.001","date_published":"2020-10-02T00:00:00Z","date_created":"2024-02-28T08:50:34Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2024-02-28T12:37:54Z","department":[{"_id":"MaLo"}],"_id":"15036","article_type":"original","type":"journal_article","status":"public","keyword":["Molecular Biology","Structural Biology"],"publication_identifier":{"issn":["0022-2836"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":432,"issue":"21","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"month":"10","intvolume":" 432"},{"date_updated":"2024-02-28T12:57:31Z","ddc":["000"],"file_date_updated":"2020-11-23T09:03:19Z","department":[{"_id":"ChWo"}],"_id":"8384","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-11-23T09:03:19Z","file_size":14935529,"date_created":"2020-11-23T09:03:19Z","file_name":"2020_soapfilm_submitted.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8795","checksum":"813831ca91319d794d9748c276b24578","success":1}],"language":[{"iso":"eng"}],"issue":"4","volume":39,"ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392405","open_access":"1"}],"month":"07","intvolume":" 39","citation":{"chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","full_name":"Ishida, Sadashige"},{"full_name":"Synak, Peter","last_name":"Synak","first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fumiya","last_name":"Narita","full_name":"Narita, Fumiya"},{"last_name":"Hachisuka","full_name":"Hachisuka, Toshiya","first_name":"Toshiya"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"external_id":{"isi":["000583700300004"]},"article_processing_charge":"No","title":"A model for soap film dynamics with evolving thickness","article_number":"31","project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"08","publication":"ACM Transactions on Graphics","date_published":"2020-07-08T00:00:00Z","doi":"10.1145/3386569.3392405","date_created":"2020-09-13T22:01:18Z","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1},{"citation":{"ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282","short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Artur","orcid":"0000-0002-5646-9524","full_name":"Czumaj, Artur","last_name":"Czumaj"},{"first_name":"Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","full_name":"Davies, Peter","orcid":"0000-0002-5646-9524"},{"first_name":"Merav","full_name":"Parter, Merav","last_name":"Parter"}],"article_processing_charge":"No","external_id":{"isi":["000744436200015"],"arxiv":["1912.05390"]},"title":"Graph sparsification for derandomizing massively parallel computation with low space","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"isi":1,"year":"2020","day":"01","publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","page":"175-185","doi":"10.1145/3350755.3400282","date_published":"2020-07-01T00:00:00Z","date_created":"2020-05-06T08:53:34Z","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"date_updated":"2024-02-28T12:53:09Z","department":[{"_id":"DaAl"}],"_id":"7802","type":"conference","conference":{"start_date":"2020-07-15","end_date":"2020-07-17","location":"Virtual Event, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9541","status":"public","relation":"later_version"}]},"issue":"7","ec_funded":1,"abstract":[{"text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17].","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1912.05390","open_access":"1"}],"month":"07"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"month":"02","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3332466.3374542","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450368186"]},"publication_status":"published","ec_funded":1,"_id":"7636","status":"public","type":"conference","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22","end_date":"2020-02-26","location":"San Diego, CA, United States"},"date_updated":"2024-02-28T12:55:14Z","department":[{"_id":"DaAl"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"19","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","isi":1,"year":"2020","doi":"10.1145/3332466.3374542","date_published":"2020-02-19T00:00:00Z","date_created":"2020-04-05T22:00:49Z","page":"276-291","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291.","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542."},"title":"Non-blocking interpolation search trees with doubly-logarithmic running time","author":[{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"},{"first_name":"Aleksandar","last_name":"Prokopec","full_name":"Prokopec, Aleksandar"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"external_id":{"isi":["000564476500020"]},"article_processing_charge":"No"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:10.1145/3350755.3400213.","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49.","ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2020, no. 7, pp. 37–49.","apa":"Alistarh, D.-A., Brown, T. A., & Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400213","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2020:37-49. doi:10.1145/3350755.3400213","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 37–49. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400213.","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49."},"date_updated":"2024-02-28T12:56:32Z","department":[{"_id":"DaAl"}],"title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"first_name":"Nandini","full_name":"Singhal, Nandini","last_name":"Singhal"}],"external_id":{"isi":["000744436200004"]},"article_processing_charge":"No","_id":"8191","status":"public","type":"conference","conference":{"location":"Virtual Event, United States","end_date":"2020-07-17","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"day":"06","publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"isbn":["9781450369350"]},"publication_status":"published","year":"2020","doi":"10.1145/3350755.3400213","issue":"7","date_published":"2020-07-06T00:00:00Z","date_created":"2020-08-02T22:00:58Z","page":"37-49","oa_version":"None","abstract":[{"lang":"eng","text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures."}],"month":"07","scopus_import":"1","publisher":"Association for Computing Machinery","quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:53:46Z","citation":{"mla":"Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–24, doi:10.1145/3332466.3374503.","ama":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency on the JVM with Lincheck. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP. Association for Computing Machinery; 2020:423-424. doi:10.1145/3332466.3374503","apa":"Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., & Tsitelov, D. (2020). Testing concurrency on the JVM with Lincheck. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP (pp. 423–424). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374503","ieee":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing concurrency on the JVM with Lincheck,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, San Diego, CA, United States, 2020, pp. 423–424.","short":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–424.","chicago":"Koval, Nikita, Mariia Sokolova, Alexander Fedorov, Dan-Adrian Alistarh, and Dmitry Tsitelov. “Testing Concurrency on the JVM with Lincheck.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, 423–24. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374503.","ista":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. 2020. Testing concurrency on the JVM with Lincheck. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP. PPOPP: Principles and Practice of Parallel Programming, 423–424."},"title":"Testing concurrency on the JVM with Lincheck","department":[{"_id":"DaAl"}],"article_processing_charge":"No","author":[{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sokolova, Mariia","last_name":"Sokolova","first_name":"Mariia","id":"26217AE4-77FF-11EA-8101-AD24D49E41F4"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"}],"_id":"7635","status":"public","conference":{"location":"San Diego, CA, United States","end_date":"2020-02-26","start_date":"2020-02-22","name":"PPOPP: Principles and Practice of Parallel Programming"},"type":"conference","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP","language":[{"iso":"eng"}],"day":"19","publication_status":"published","year":"2020","publication_identifier":{"isbn":["9781450368186"]},"date_created":"2020-04-05T22:00:48Z","doi":"10.1145/3332466.3374503","date_published":"2020-02-19T00:00:00Z","page":"423-424","oa_version":"None","abstract":[{"text":"Concurrent programming can be notoriously complex and error-prone. Programming bugs can arise from a variety of sources, such as operation re-reordering, or incomplete understanding of the memory model. A variety of formal and model checking methods have been developed to address this fundamental difficulty. While technically interesting, existing academic methods are still hard to apply to the large codebases typical of industrial deployments, which limits their practical impact.","lang":"eng"}],"month":"02","quality_controlled":"1","scopus_import":"1","publisher":"Association for Computing Machinery"},{"_id":"8383","status":"public","conference":{"start_date":"2020-08-03","location":"Virtual, Italy","end_date":"2020-08-07","name":"PODC: Principles of Distributed Computing"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:54:19Z","citation":{"short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement: Why Extension-Based Proofs Fail,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 54–56.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement: Why Extension-Based Proofs Fail. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:54-56. doi:10.1145/3382734.3405743","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2020). Brief Announcement: Why Extension-Based Proofs Fail. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 54–56). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405743","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs Fail.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56, doi:10.1145/3382734.3405743.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement: Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 54–56.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 54–56. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405743."},"department":[{"_id":"DaAl"}],"title":"Brief Announcement: Why Extension-Based Proofs Fail","article_processing_charge":"No","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"first_name":"Faith","full_name":"Ellen, Faith","last_name":"Ellen"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"first_name":"Leqi","last_name":"Zhu","full_name":"Zhu, Leqi"}],"oa_version":"None","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We explain why this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.","lang":"eng"}],"month":"07","quality_controlled":"1","publisher":"Association for Computing Machinery","scopus_import":"1","publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","language":[{"iso":"eng"}],"day":"31","publication_status":"published","year":"2020","publication_identifier":{"isbn":["9781450375825"]},"date_created":"2020-09-13T22:01:18Z","doi":"10.1145/3382734.3405743","date_published":"2020-07-31T00:00:00Z","page":"54-56"},{"status":"public","article_type":"original","type":"journal_article","_id":"8385","file_date_updated":"2020-11-23T09:01:22Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2024-02-28T12:57:47Z","intvolume":" 39","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392412"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"ec_funded":1,"volume":39,"related_material":{"record":[{"relation":"dissertation_contains","id":"12358","status":"public"}]},"issue":"4","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-11-23T09:01:22Z","file_size":38922662,"creator":"dernst","date_created":"2020-11-23T09:01:22Z","file_name":"2020_hylc_submitted.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8794","checksum":"cf4c1d361c3196c4bd424520a5588205","success":1}],"publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"48","title":"Homogenized yarn-level cloth","article_processing_charge":"No","external_id":{"isi":["000583700300021"]},"author":[{"full_name":"Sperl, Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"full_name":"Narain, Rahul","last_name":"Narain","first_name":"Rahul"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392412","apa":"Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392412."},"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","date_created":"2020-09-13T22:01:18Z","date_published":"2020-07-08T00:00:00Z","doi":"10.1145/3386569.3392412","publication":"ACM Transactions on Graphics","day":"08","year":"2020","has_accepted_license":"1","isi":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.","ista":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 152(20), 204905.","mla":"Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no. 20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194.","apa":"Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194","ama":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 2020;152(20). doi:10.1063/5.0005194","ieee":"J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering in systems with competing interactions: A machine learning study,” The Journal of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.","short":"J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical Physics 152 (2020)."},"title":"Shear-induced ordering in systems with competing interactions: A machine learning study","author":[{"last_name":"Pȩkalski","full_name":"Pȩkalski, J.","first_name":"J."},{"orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"},{"first_name":"A. Z.","last_name":"Panagiotopoulos","full_name":"Panagiotopoulos, A. Z."}],"external_id":{"arxiv":["2002.07294"],"isi":["000537900300001"]},"article_processing_charge":"No","article_number":"204905","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"day":"29","publication":"The Journal of chemical physics","isi":1,"year":"2020","doi":"10.1063/5.0005194","date_published":"2020-05-29T00:00:00Z","date_created":"2020-06-14T22:00:49Z","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"date_updated":"2024-02-28T13:00:28Z","department":[{"_id":"MiLe"}],"_id":"7956","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10897690"]},"publication_status":"published","issue":"20","volume":152,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.","lang":"eng"}],"month":"05","intvolume":" 152","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0005194"}]},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"year":"2020","day":"13","publication":"Physical Review B","doi":"10.1103/PhysRevB.101.020504","date_published":"2020-01-13T00:00:00Z","date_created":"2020-02-02T23:01:01Z","article_number":"020504","citation":{"ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.020504.","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” Physical Review B, vol. 101, no. 2. American Physical Society, 2020.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020).","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"first_name":"P. L.S.","full_name":"Lopes, P. L.S.","last_name":"Lopes"},{"first_name":"Pavan","last_name":"Hosur","full_name":"Hosur, Pavan"},{"full_name":"Gilbert, Matthew J.","last_name":"Gilbert","first_name":"Matthew J."},{"last_name":"Ghaemi","full_name":"Ghaemi, Pouyan","first_name":"Pouyan"}],"article_processing_charge":"No","external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","abstract":[{"text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"month":"01","intvolume":" 101","publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":101,"issue":"2","_id":"7428","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-02-28T13:11:13Z","department":[{"_id":"MiLe"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224."},"title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","article_processing_charge":"No","external_id":{"isi":["000555104200011"],"arxiv":["1912.08334"]},"author":[{"first_name":"Yunfan","full_name":"Wu, Yunfan","last_name":"Wu"},{"first_name":"Rajiv","full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar"},{"last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián","first_name":"Julián"},{"full_name":"Malia, Benjamin K.","last_name":"Malia","first_name":"Benjamin K."},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur"},{"last_name":"Kasevich","full_name":"Kasevich, Mark A.","first_name":"Mark A."}],"article_number":"012224","publication":"Physical Review A","day":"30","year":"2020","isi":1,"date_created":"2020-08-30T22:01:10Z","date_published":"2020-07-30T00:00:00Z","doi":"10.1103/PhysRevA.102.012224","acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_updated":"2024-02-28T13:11:28Z","department":[{"_id":"OnHo"}],"_id":"8319","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"issue":"1","volume":102,"oa_version":"Preprint","abstract":[{"text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.","lang":"eng"}],"intvolume":" 102","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1912.08334","open_access":"1"}],"scopus_import":"1"},{"doi":"10.1111/cgf.14100","date_published":"2020-12-01T00:00:00Z","date_created":"2020-11-17T10:47:48Z","page":"47-54","day":"01","publication":"Computer Graphics forum","isi":1,"year":"2020","quality_controlled":"1","publisher":"Wiley","title":"Making procedural water waves boundary-aware","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"},{"first_name":"Nuttapong","last_name":"Chentanez","full_name":"Chentanez, Nuttapong"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"first_name":"Matthias","full_name":"Müller-Fischer, Matthias","last_name":"Müller-Fischer"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"article_processing_charge":"No","external_id":{"isi":["000591780400005"]},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C. Wojtan, “Making procedural water waves boundary-aware,” Computer Graphics forum, vol. 39, no. 8. Wiley, pp. 47–54, 2020.","short":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan, Computer Graphics Forum 39 (2020) 47–54.","apa":"Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., & Wojtan, C. (2020). Making procedural water waves boundary-aware. Computer Graphics Forum. Online Symposium: Wiley. https://doi.org/10.1111/cgf.14100","ama":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making procedural water waves boundary-aware. Computer Graphics forum. 2020;39(8):47-54. doi:10.1111/cgf.14100","mla":"Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” Computer Graphics Forum, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:10.1111/cgf.14100.","ista":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020. Making procedural water waves boundary-aware. Computer Graphics forum. 39(8), 47–54.","chicago":"Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin, Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.14100."},"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"issue":"8","volume":39,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"12","intvolume":" 39","scopus_import":"1","oa_version":"None","abstract":[{"text":"The “procedural” approach to animating ocean waves is the dominant algorithm for animating larger bodies of water in\r\ninteractive applications as well as in off-line productions — it provides high visual quality with a low computational demand. In this paper, we widen the applicability of procedural water wave animation with an extension that guarantees the satisfaction of boundary conditions imposed by terrain while still approximating physical wave behavior. In combination with a particle system that models wave breaking, foam, and spray, this allows us to naturally model waves interacting with beaches and rocks. Our system is able to animate waves at large scales at interactive frame rates on a commodity PC.","lang":"eng"}],"department":[{"_id":"ChWo"},{"_id":"BeBi"}],"date_updated":"2024-02-28T13:58:11Z","status":"public","type":"journal_article","article_type":"original","conference":{"start_date":"2020-10-06","location":"Online Symposium","end_date":"2020-10-09","name":"SCA: Symposium on Computer Animation"},"_id":"8766"},{"department":[{"_id":"KrCh"}],"date_updated":"2024-03-04T08:30:16Z","status":"public","keyword":["General Medicine"],"article_type":"original","type":"journal_article","conference":{"start_date":"2020-02-07","location":"New York, NY, United States","end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence"},"_id":"15055","volume":34,"issue":"06","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2374-3468"]},"publication_status":"published","month":"04","intvolume":" 34","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2002.12086"}],"oa_version":"Preprint","abstract":[{"text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.","lang":"eng"}],"title":"Reinforcement learning of risk-constrained policies in Markov decision processes","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr"},{"first_name":"Jiří","full_name":"Vahala, Jiří","last_name":"Vahala"}],"article_processing_charge":"No","external_id":{"arxiv":["2002.12086"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531","apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531"},"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"}],"doi":"10.1609/aaai.v34i06.6531","date_published":"2020-04-03T00:00:00Z","date_created":"2024-03-04T08:07:22Z","page":"9794-9801","day":"03","publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","year":"2020","publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","oa":1,"acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y."},{"oa_version":"Published Version","abstract":[{"text":"Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans.","lang":"eng"}],"month":"07","intvolume":" 6","file":[{"file_size":1864415,"date_updated":"2024-03-04T09:46:41Z","creator":"dernst","file_name":"2020_ScienceAdvances_Park.pdf","date_created":"2024-03-04T09:46:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"a37157cd0de709dce5fe03f4a31cd0b6","file_id":"15058"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","issue":"27","volume":6,"_id":"15057","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["570"],"date_updated":"2024-03-04T09:52:09Z","file_date_updated":"2024-03-04T09:46:41Z","department":[{"_id":"MaDe"}],"acknowledgement":"This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366 funded by the Korean Government (MSIT) through the National Research Foundation (NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440) funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. ","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"day":"01","publication":"Science Advances","has_accepted_license":"1","year":"2020","doi":"10.1126/sciadv.aaw7824","date_published":"2020-07-01T00:00:00Z","date_created":"2024-03-04T09:41:57Z","article_number":"aaw7824","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances, vol. 6, no. 27, aaw7824, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.","ieee":"S. Park et al., “VRK-1 extends life span by activation of AMPK via phosphorylation,” Science Advances, vol. 6, no. 27. American Association for the Advancement of Science, 2020.","short":"S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin, K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020).","apa":"Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., … Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw7824","ama":"Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824","chicago":"Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung, Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.","ista":"Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation. Science Advances. 6(27), aaw7824."},"title":"VRK-1 extends life span by activation of AMPK via phosphorylation","author":[{"first_name":"Sangsoon","full_name":"Park, Sangsoon","last_name":"Park"},{"last_name":"Artan","full_name":"Artan, Murat","orcid":"0000-0001-8945-6992","id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat"},{"last_name":"Han","full_name":"Han, Seung Hyun","first_name":"Seung Hyun"},{"first_name":"Hae-Eun H.","last_name":"Park","full_name":"Park, Hae-Eun H."},{"full_name":"Jung, Yoonji","last_name":"Jung","first_name":"Yoonji"},{"last_name":"Hwang","full_name":"Hwang, Ara B.","first_name":"Ara B."},{"first_name":"Won Sik","last_name":"Shin","full_name":"Shin, Won Sik"},{"last_name":"Kim","full_name":"Kim, Kyong-Tai","first_name":"Kyong-Tai"},{"last_name":"Lee","full_name":"Lee, Seung-Jae V.","first_name":"Seung-Jae V."}],"article_processing_charge":"No"},{"acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. ","oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","day":"08","year":"2020","date_created":"2024-03-04T10:03:52Z","date_published":"2020-09-08T00:00:00Z","doi":"10.1073/pnas.1917269117","page":"22101-22112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117","ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112."},"title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","external_id":{"pmid":["32848067"]},"article_processing_charge":"No","author":[{"full_name":"Pinotsis, Nikos","last_name":"Pinotsis","first_name":"Nikos"},{"first_name":"Karolina","full_name":"Zielinska, Karolina","last_name":"Zielinska"},{"first_name":"Mrigya","last_name":"Babuta","full_name":"Babuta, Mrigya"},{"first_name":"Joan L.","full_name":"Arolas, Joan L.","last_name":"Arolas"},{"first_name":"Julius","full_name":"Kostan, Julius","last_name":"Kostan"},{"first_name":"Muhammad Bashir","last_name":"Khan","full_name":"Khan, Muhammad Bashir"},{"full_name":"Schreiner, Claudia","last_name":"Schreiner","first_name":"Claudia"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"full_name":"Ciccarelli, Luciano","last_name":"Ciccarelli","first_name":"Luciano"},{"last_name":"Puchinger","full_name":"Puchinger, Martin","first_name":"Martin"},{"first_name":"Eirini A.","last_name":"Gkougkoulia","full_name":"Gkougkoulia, Eirini A."},{"first_name":"Euripedes de Almeida","last_name":"Ribeiro","full_name":"Ribeiro, Euripedes de Almeida"},{"last_name":"Marlovits","full_name":"Marlovits, Thomas C.","first_name":"Thomas C."},{"full_name":"Bhattacharya, Alok","last_name":"Bhattacharya","first_name":"Alok"},{"full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo","first_name":"Kristina"}],"oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.","lang":"eng"}],"intvolume":" 117","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.191726911"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"volume":117,"issue":"36","_id":"15061","status":"public","article_type":"original","type":"journal_article","date_updated":"2024-03-04T10:14:44Z","department":[{"_id":"CaBe"}]},{"date_updated":"2024-03-04T10:54:04Z","ddc":["500"],"file_date_updated":"2024-03-04T10:52:42Z","department":[{"_id":"HeEd"}],"_id":"15064","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2024-03-04T10:52:42Z","file_name":"2020_JourApplCompTopology_Bauer.pdf","creator":"dernst","date_updated":"2024-03-04T10:52:42Z","file_size":851190,"file_id":"15065","checksum":"eed1168b6e66cd55272c19bb7fca8a1c","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"issue":"4","volume":4,"abstract":[{"lang":"eng","text":"We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 4","month":"12","citation":{"ista":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 4(4), 455–480.","chicago":"Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8.","ieee":"U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient flow and homology inference for self-maps,” Journal of Applied and Computational Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.","short":"U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and Computational Topology 4 (2020) 455–480.","apa":"Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8","ama":"Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow and homology inference for self-maps. Journal of Applied and Computational Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8","mla":"Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and Computational Topology, vol. 4, no. 4, Springer Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"U.","last_name":"Bauer","full_name":"Bauer, U."},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz"},{"first_name":"M.","full_name":"Mrozek, M.","last_name":"Mrozek"}],"title":"Čech-Delaunay gradient flow and homology inference for self-maps","year":"2020","has_accepted_license":"1","publication":"Journal of Applied and Computational Topology","day":"01","page":"455-480","date_created":"2024-03-04T10:47:49Z","date_published":"2020-12-01T00:00:00Z","doi":"10.1007/s41468-020-00058-8","acknowledgement":"This research has been supported by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding provided by Projekt DEAL.","oa":1,"publisher":"Springer Nature","quality_controlled":"1"}]