[{"publication":"Communications Physics","department":[{"_id":"MiLe"}],"title":"Generation of spin currents by a temperature gradient in a two-terminal device","publisher":"Springer Nature","date_created":"2021-12-05T23:01:39Z","ec_funded":1,"oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect."}],"volume":4,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"10401","has_accepted_license":"1","year":"2021","acknowledgement":"The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z).","status":"public","oa":1,"issue":"1","article_type":"original","external_id":{"arxiv":["2101.02020"],"isi":["10.1038/s42005-021-00753-7"]},"citation":{"chicago":"Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” <i>Communications Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s42005-021-00753-7\">https://doi.org/10.1038/s42005-021-00753-7</a>.","ieee":"R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” <i>Communications Physics</i>, vol. 4, no. 1. Springer Nature, 2021.","apa":"Barfknecht, R. E., Foerster, A., Zinner, N. T., &#38; Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-021-00753-7\">https://doi.org/10.1038/s42005-021-00753-7</a>","ama":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. <i>Communications Physics</i>. 2021;4(1). doi:<a href=\"https://doi.org/10.1038/s42005-021-00753-7\">10.1038/s42005-021-00753-7</a>","short":"R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021).","ista":"Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252.","mla":"Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” <i>Communications Physics</i>, vol. 4, no. 1, 252, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s42005-021-00753-7\">10.1038/s42005-021-00753-7</a>."},"publication_identifier":{"eissn":["23993650"]},"file_date_updated":"2021-12-06T14:53:41Z","article_number":"252","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Barfknecht, Rafael E.","first_name":"Rafael E.","last_name":"Barfknecht"},{"last_name":"Foerster","first_name":"Angela","full_name":"Foerster, Angela"},{"last_name":"Zinner","first_name":"Nikolaj T.","full_name":"Zinner, Nikolaj T."},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem"}],"date_published":"2021-11-26T00:00:00Z","article_processing_charge":"No","doi":"10.1038/s42005-021-00753-7","date_updated":"2023-08-14T13:04:34Z","scopus_import":"1","quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"         4","file":[{"date_updated":"2021-12-06T14:53:41Z","file_id":"10420","file_size":1068984,"checksum":"9097319952cb9a3d96e7fd3aa9813a03","file_name":"2021_NatComm_Barfknecht.pdf","relation":"main_file","access_level":"open_access","creator":"alisjak","content_type":"application/pdf","date_created":"2021-12-06T14:53:41Z","success":1}],"publication_status":"published","ddc":["530"],"day":"26","month":"11","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"language":[{"iso":"eng"}]},{"date_created":"2021-12-05T23:01:40Z","ec_funded":1,"oa_version":"Published Version","publication":"Nature Communications","department":[{"_id":"EdHa"}],"title":"Theory of branching morphogenesis by local interactions and global guidance","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales."}],"_id":"10402","has_accepted_license":"1","year":"2021","volume":12,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","citation":{"apa":"Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>","ieee":"M. C. Ucar <i>et al.</i>, “Theory of branching morphogenesis by local interactions and global guidance,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","chicago":"Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27135-5\">https://doi.org/10.1038/s41467-021-27135-5</a>.","mla":"Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” <i>Nature Communications</i>, vol. 12, 6830, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>.","ista":"Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830.","short":"M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021).","ama":"Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-27135-5\">10.1038/s41467-021-27135-5</a>"},"publication_identifier":{"eissn":["2041-1723"]},"status":"public","acknowledgement":"We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.).","oa":1,"article_type":"original","external_id":{"pmid":["34819507"],"isi":["000722322900020"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2021-12-10T08:54:09Z","article_number":"6830","scopus_import":"1","quality_controlled":"1","date_published":"2021-11-24T00:00:00Z","author":[{"first_name":"Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"last_name":"Kamenev","first_name":"Dmitrii","full_name":"Kamenev, Dmitrii"},{"last_name":"Sunadome","first_name":"Kazunori","full_name":"Sunadome, Kazunori"},{"full_name":"Fachet, Dominik C","id":"14FDD550-AA41-11E9-A0E5-1ACCE5697425","first_name":"Dominik C","last_name":"Fachet"},{"first_name":"Francois","last_name":"Lallemend","full_name":"Lallemend, Francois"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"},{"full_name":"Hadjab, Saida","first_name":"Saida","last_name":"Hadjab"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","related_material":{"record":[{"id":"13058","status":"public","relation":"research_data"}]},"date_updated":"2023-08-14T13:18:46Z","doi":"10.1038/s41467-021-27135-5","intvolume":"        12","file":[{"relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-10T08:54:09Z","success":1,"date_updated":"2021-12-10T08:54:09Z","file_id":"10529","file_size":2303405,"checksum":"63c56ec75314a71e63e7dd2920b3c5b5","file_name":"2021_NatComm_Ucar.pdf"}],"publication_status":"published","isi":1,"month":"11","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"pmid":1,"ddc":["573"],"day":"24"},{"date_published":"2021-11-03T00:00:00Z","author":[{"full_name":"Biane, Celia","last_name":"Biane","first_name":"Celia"},{"first_name":"Florian","last_name":"Rückerl","full_name":"Rückerl, Florian"},{"full_name":"Abrahamsson, Therese","last_name":"Abrahamsson","first_name":"Therese"},{"first_name":"Cécile","last_name":"Saint-Cloment","full_name":"Saint-Cloment, Cécile"},{"first_name":"Jean","last_name":"Mariani","full_name":"Mariani, Jean"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Digregorio, David A.","first_name":"David A.","last_name":"Digregorio"},{"full_name":"Sherrard, Rachel M.","last_name":"Sherrard","first_name":"Rachel M."},{"last_name":"Cathala","first_name":"Laurence","full_name":"Cathala, Laurence"}],"article_processing_charge":"No","doi":"10.7554/eLife.65954","date_updated":"2023-08-14T13:12:07Z","scopus_import":"1","quality_controlled":"1","file_date_updated":"2021-12-10T08:31:41Z","article_number":"e65954","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"day":"03","month":"11","isi":1,"language":[{"iso":"eng"}],"intvolume":"        10","file":[{"relation":"main_file","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-10T08:31:41Z","success":1,"file_id":"10528","date_updated":"2021-12-10T08:31:41Z","file_size":13131322,"checksum":"c7c33c3319428d56e332e22349c50ed3","file_name":"2021_eLife_Biane.pdf"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits."}],"publication":"eLife","title":"Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons","department":[{"_id":"RySh"}],"publisher":"eLife Sciences Publications","date_created":"2021-12-05T23:01:40Z","oa_version":"Published Version","status":"public","acknowledgement":"This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript.","oa":1,"external_id":{"isi":["000715789500001"]},"article_type":"original","citation":{"apa":"Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.65954\">https://doi.org/10.7554/eLife.65954</a>","chicago":"Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.65954\">https://doi.org/10.7554/eLife.65954</a>.","ieee":"C. Biane <i>et al.</i>, “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021).","mla":"Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” <i>ELife</i>, vol. 10, e65954, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.65954\">10.7554/eLife.65954</a>.","ista":"Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954.","ama":"Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.65954\">10.7554/eLife.65954</a>"},"publication_identifier":{"eissn":["2050-084X"]},"volume":10,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"10403","has_accepted_license":"1","year":"2021"},{"scopus_import":"1","quality_controlled":"1","author":[{"first_name":"Stefan","last_name":"Sietzen","full_name":"Sietzen, Stefan"},{"first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Borowski, Judy","first_name":"Judy","last_name":"Borowski"},{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"first_name":"Manuela","last_name":"Waldner","full_name":"Waldner, Manuela"}],"date_published":"2021-11-27T00:00:00Z","date_updated":"2023-08-14T13:11:42Z","doi":"10.1111/cgf.14418","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/2110.07667","open_access":"1"}],"intvolume":"        40","publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"11","isi":1,"day":"27","oa_version":"Preprint","date_created":"2021-12-05T23:01:40Z","title":"Interactive analysis of CNN robustness","department":[{"_id":"ToHe"}],"publication":"Computer Graphics Forum","publisher":"Wiley","abstract":[{"text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models.","lang":"eng"}],"arxiv":1,"_id":"10404","year":"2021","page":"253-264","volume":40,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. <i>Computer Graphics Forum</i>. 2021;40(7):253-264. doi:<a href=\"https://doi.org/10.1111/cgf.14418\">10.1111/cgf.14418</a>","ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” <i>Computer Graphics Forum</i>, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:<a href=\"https://doi.org/10.1111/cgf.14418\">10.1111/cgf.14418</a>.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” <i>Computer Graphics Forum</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/cgf.14418\">https://doi.org/10.1111/cgf.14418</a>.","ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” <i>Computer Graphics Forum</i>, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., &#38; Waldner, M. (2021). Interactive analysis of CNN robustness. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14418\">https://doi.org/10.1111/cgf.14418</a>"},"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","status":"public","oa":1,"article_type":"original","external_id":{"isi":["000722952000024"],"arxiv":["2110.07667"]},"issue":"7"},{"abstract":[{"lang":"eng","text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future."}],"publisher":"Annual Reviews","department":[{"_id":"CaHe"}],"title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","publication":"Annual Review of Genetics","oa_version":"None","date_created":"2021-12-05T23:01:41Z","ec_funded":1,"external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"article_type":"original","acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","status":"public","publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"citation":{"ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” <i>Annual Review of Genetics</i>, vol. 55. Annual Reviews, pp. 209–233, 2021.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” <i>Annual Review of Genetics</i>. Annual Reviews, 2021. <a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">https://doi.org/10.1146/annurev-genet-071819-103748</a>.","apa":"Mishra, N., &#38; Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. <i>Annual Review of Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">https://doi.org/10.1146/annurev-genet-071819-103748</a>","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. <i>Annual Review of Genetics</i>. 2021;55:209-233. doi:<a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">10.1146/annurev-genet-071819-103748</a>","ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” <i>Annual Review of Genetics</i>, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:<a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">10.1146/annurev-genet-071819-103748</a>.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233."},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"209-233","volume":55,"year":"2021","_id":"10406","doi":"10.1146/annurev-genet-071819-103748","date_updated":"2023-08-14T13:05:13Z","article_processing_charge":"No","author":[{"id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","last_name":"Mishra","first_name":"Nikhil"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2021-08-30T00:00:00Z","quality_controlled":"1","scopus_import":"1","keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"day":"30","pmid":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"08","isi":1,"publication_status":"published","intvolume":"        55"},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"]},"citation":{"ista":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.","mla":"Chakraborty, Suvradip, et al. <i>Trojan-Resilience without Cryptography</i>. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">10.1007/978-3-030-90453-1_14</a>.","short":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428.","ama":"Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">10.1007/978-3-030-90453-1_14</a>","apa":"Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., &#38; Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">https://doi.org/10.1007/978-3-030-90453-1_14</a>","ieee":"S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_14\">https://doi.org/10.1007/978-3-030-90453-1_14</a>."},"external_id":{"isi":["000728364000014"]},"status":"public","oa":1,"year":"2021","_id":"10407","type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"397-428","volume":13043,"abstract":[{"lang":"eng","text":"Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification   F  one has more sophisticated circuits   F⋄  manufactured (where   F⋄  specifies a MPC or VC of   F ), and then embeds these   F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to   F . Those solutions impose a significant overhead as   F⋄  is much more complex than   F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where   F  has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e.,   F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of   F  need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound."}],"oa_version":"Preprint","ec_funded":1,"date_created":"2021-12-05T23:01:42Z","publisher":"Springer Nature","title":"Trojan-resilience without cryptography","department":[{"_id":"KrPi"}],"project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"isi":1,"month":"11","day":"04","publication_status":"published","main_file_link":[{"url":"https://eprint.iacr.org/2021/1224","open_access":"1"}],"intvolume":"     13043","quality_controlled":"1","scopus_import":"1","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-90453-1_14","date_updated":"2023-08-14T13:07:46Z","article_processing_charge":"No","date_published":"2021-11-04T00:00:00Z","author":[{"full_name":"Chakraborty, Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","first_name":"Suvradip","last_name":"Chakraborty"},{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"last_name":"Gałązka","first_name":"Małgorzata","full_name":"Gałązka, Małgorzata"},{"last_name":"Lizurej","first_name":"Tomasz","full_name":"Lizurej, Tomasz"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michelle X","last_name":"Yeo","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"conference":{"end_date":"2021-11-11","name":"TCC: Theory of Cryptography Conference","start_date":"2021-11-08","location":"Raleigh, NC, United States"}},{"conference":{"start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11","name":"TCC: Theory of Cryptography"},"doi":"10.1007/978-3-030-90456-2_8","date_updated":"2023-08-14T13:19:39Z","alternative_title":["LNCS"],"article_processing_charge":"No","date_published":"2021-11-04T00:00:00Z","author":[{"first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","full_name":"Auerbach, Benedikt","last_name":"Auerbach","orcid":"0000-0002-7553-6606","first_name":"Benedikt"},{"last_name":"Baig","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","full_name":"Baig, Mirza Ahad"},{"last_name":"Cueto Noval","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel"},{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","full_name":"Pascual Perez, Guillermo"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","first_name":"Michael"}],"quality_controlled":"1","scopus_import":"1","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/1158"}],"intvolume":"     13044","day":"04","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"month":"11","isi":1,"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"title":"Grafting key trees: Efficient key management for overlapping groups","publication":"19th International Conference","oa_version":"Preprint","ec_funded":1,"date_created":"2021-12-05T23:01:42Z","abstract":[{"lang":"eng","text":"Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds   log(N)  keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting   2log(N)  ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks."}],"type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"222-253","volume":13044,"year":"2021","_id":"10408","external_id":{"isi":["000728363700008"]},"oa":1,"status":"public","acknowledgement":"B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","publication_identifier":{"isbn":["9-783-0309-0455-5"],"eissn":["1611-3349"],"eisbn":["978-3-030-90456-2"],"issn":["0302-9743"]},"citation":{"ama":"Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: <i>19th International Conference</i>. Vol 13044. Springer Nature; 2021:222-253. doi:<a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">10.1007/978-3-030-90456-2_8</a>","short":"J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253.","ista":"Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.","mla":"Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” <i>19th International Conference</i>, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:<a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">10.1007/978-3-030-90456-2_8</a>.","chicago":"Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In <i>19th International Conference</i>, 13044:222–53. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">https://doi.org/10.1007/978-3-030-90456-2_8</a>.","ieee":"J. F. Alwen <i>et al.</i>, “Grafting key trees: Efficient key management for overlapping groups,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.","apa":"Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In <i>19th International Conference</i> (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90456-2_8\">https://doi.org/10.1007/978-3-030-90456-2_8</a>"}},{"external_id":{"isi":["000728364000017"]},"status":"public","acknowledgement":"We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably.","oa":1,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9-783-0309-0452-4"]},"citation":{"short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517.","mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” <i>19th International Conference</i>, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">10.1007/978-3-030-90453-1_17</a>.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: <i>19th International Conference</i>. Vol 13043. Springer Nature; 2021:486-517. doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">10.1007/978-3-030-90453-1_17</a>","apa":"Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In <i>19th International Conference</i> (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">https://doi.org/10.1007/978-3-030-90453-1_17</a>","ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In <i>19th International Conference</i>, 13043:486–517. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_17\">https://doi.org/10.1007/978-3-030-90453-1_17</a>."},"type":"conference","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"486-517","volume":"13043 ","year":"2021","_id":"10409","abstract":[{"text":"We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size   S  and treewidth   w  with only a   SO(w)  loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly   O(δwlog(S)) ,   δ  being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.  with only a   SO(w)  loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly   O(δwlog(S)) ,   δ  being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.","lang":"eng"}],"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"title":"On treewidth, separators and Yao’s garbling","publication":"19th International Conference","oa_version":"Preprint","date_created":"2021-12-05T23:01:43Z","ec_funded":1,"day":"04","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"11","isi":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2021/926"}],"date_updated":"2023-08-17T06:21:38Z","related_material":{"record":[{"id":"10044","status":"public","relation":"earlier_version"}]},"doi":"10.1007/978-3-030-90453-1_17","alternative_title":["LNCS"],"article_processing_charge":"No","date_published":"2021-11-04T00:00:00Z","author":[{"first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","scopus_import":"1","conference":{"end_date":"2021-11-11","name":"TCC: Theory of Cryptography","start_date":"2021-11-08","location":"Raleigh, NC, United States"}},{"main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"intvolume":"     13043","publication_status":"published","day":"04","month":"11","isi":1,"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2021-11-08","location":"Raleigh, NC, United States","end_date":"2021-11-11","name":"TCC: Theory of Cryptography"},"date_published":"2021-11-04T00:00:00Z","author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Walter","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","alternative_title":["LNCS"],"doi":"10.1007/978-3-030-90453-1_19","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10048"}]},"date_updated":"2023-10-17T09:24:07Z","scopus_import":"1","quality_controlled":"1","volume":13043,"page":"550-581","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"conference","_id":"10410","year":"2021","oa":1,"status":"public","acknowledgement":"C. Kamath—Supported by Azrieli International Postdoctoral Fellowship. Most of the work was done while the author was at Northeastern University and Charles University, funded by the IARPA grant IARPA/2019-19-020700009 and project PRIMUS/17/SCI/9, respectively. K. Klein—Supported in part by ERC CoG grant 724307. Most of the work was done while the author was at IST Austria funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). K. Pietrzak—Funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","external_id":{"isi":["000728364000019"]},"citation":{"apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Walter, M. (2021). The cost of adaptivity in security games on graphs. In <i>19th International Conference</i> (Vol. 13043, pp. 550–581). Raleigh, NC, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">https://doi.org/10.1007/978-3-030-90453-1_19</a>","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In <i>19th International Conference</i>, 13043:550–81. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">https://doi.org/10.1007/978-3-030-90453-1_19</a>.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in <i>19th International Conference</i>, Raleigh, NC, United States, 2021, vol. 13043, pp. 550–581.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 550–581.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” <i>19th International Conference</i>, vol. 13043, Springer Nature, 2021, pp. 550–81, doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">10.1007/978-3-030-90453-1_19</a>.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 550–581.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: <i>19th International Conference</i>. Vol 13043. Springer Nature; 2021:550-581. doi:<a href=\"https://doi.org/10.1007/978-3-030-90453-1_19\">10.1007/978-3-030-90453-1_19</a>"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0309-0452-4"]},"publication":"19th International Conference","department":[{"_id":"KrPi"}],"title":"The cost of adaptivity in security games on graphs","publisher":"Springer Nature","ec_funded":1,"date_created":"2021-12-05T23:01:43Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical framework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower bounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and broadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques."}]},{"date_created":"2021-12-05T23:01:45Z","ec_funded":1,"oa_version":"Preprint","publication":"24th International Symposium on Formal Methods","department":[{"_id":"KrCh"}],"title":"On lexicographic proof rules for probabilistic termination","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in LexRSM not existing even for simple terminating programs. Our contributions are twofold: First, we introduce a generalization of LexRSMs which allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs."}],"arxiv":1,"_id":"10414","year":"2021","volume":13047,"page":"619-639","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","citation":{"chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” In <i>24th International Symposium on Formal Methods</i>, 13047:619–39. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">https://doi.org/10.1007/978-3-030-90870-6_33</a>.","ieee":"K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” in <i>24th International Symposium on Formal Methods</i>, Virtual, 2021, vol. 13047, pp. 619–639.","apa":"Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., &#38; Zikelic, D. (2021). On lexicographic proof rules for probabilistic termination. In <i>24th International Symposium on Formal Methods</i> (Vol. 13047, pp. 619–639). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">https://doi.org/10.1007/978-3-030-90870-6_33</a>","ama":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. In: <i>24th International Symposium on Formal Methods</i>. Vol 13047. Springer Nature; 2021:619-639. doi:<a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">10.1007/978-3-030-90870-6_33</a>","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>24th International Symposium on Formal Methods</i>, vol. 13047, Springer Nature, 2021, pp. 619–39, doi:<a href=\"https://doi.org/10.1007/978-3-030-90870-6_33\">10.1007/978-3-030-90870-6_33</a>.","short":"K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:, 24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.","ista":"Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. 2021. On lexicographic proof rules for probabilistic termination. 24th International Symposium on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639."},"publication_identifier":{"eisbn":["978-3-030-90870-6"],"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9-783-0309-0869-0"]},"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","status":"public","oa":1,"external_id":{"arxiv":["2108.02188"],"isi":["000758218600033"]},"conference":{"start_date":"2021-11-20","location":"Virtual","end_date":"2021-11-26","name":"FM: Formal Methods"},"scopus_import":"1","quality_controlled":"1","date_published":"2021-11-10T00:00:00Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"},{"full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný"},{"last_name":"Zárevúcky","first_name":"Jiří","full_name":"Zárevúcky, Jiří"},{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"article_processing_charge":"No","related_material":{"record":[{"id":"14539","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"later_version","id":"14778"}]},"doi":"10.1007/978-3-030-90870-6_33","date_updated":"2025-07-14T09:10:11Z","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.02188"}],"intvolume":"     13047","publication_status":"published","month":"11","isi":1,"language":[{"iso":"eng"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"day":"10"},{"article_processing_charge":"No","alternative_title":["Progress in Mathematics"],"doi":"10.1007/978-3-030-86872-7","date_updated":"2022-06-03T07:38:33Z","author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177"}],"date_published":"2021-12-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"The Hardy–Littlewood circle method was invented over a century ago to study integer solutions to special Diophantine equations, but it has since proven to be one of the most successful all-purpose tools available to number theorists. Not only is it capable of handling remarkably general systems of polynomial equations defined over arbitrary global fields, but it can also shed light on the space of rational curves that lie on algebraic varieties.  This book, in which the arithmetic of cubic polynomials takes centre stage, is aimed at bringing beginning graduate students into contact with some of the many facets of the circle method, both classical and modern. This monograph is the winner of the 2021 Ferran Sunyer i Balaguer Prize, a prestigious award for books of expository nature presenting the latest developments in an active area of research in mathematics."}],"publisher":"Springer Nature","title":"Cubic Forms and the Circle Method","department":[{"_id":"TiBr"}],"date_created":"2021-12-05T23:01:46Z","oa_version":"None","day":"01","status":"public","month":"12","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-030-86871-0"],"eissn":["2296-505X"],"eisbn":["978-3-030-86872-7"],"issn":["0743-1643"]},"citation":{"chicago":"Browning, Timothy D. <i>Cubic Forms and the Circle Method</i>. Vol. 343. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-86872-7\">https://doi.org/10.1007/978-3-030-86872-7</a>.","ieee":"T. D. Browning, <i>Cubic Forms and the Circle Method</i>, vol. 343. Cham: Springer Nature, 2021.","apa":"Browning, T. D. (2021). <i>Cubic Forms and the Circle Method</i> (Vol. 343). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-86872-7\">https://doi.org/10.1007/978-3-030-86872-7</a>","ama":"Browning TD. <i>Cubic Forms and the Circle Method</i>. Vol 343. Cham: Springer Nature; 2021. doi:<a href=\"https://doi.org/10.1007/978-3-030-86872-7\">10.1007/978-3-030-86872-7</a>","ista":"Browning TD. 2021. Cubic Forms and the Circle Method, Cham: Springer Nature, XIV, 166p.","mla":"Browning, Timothy D. <i>Cubic Forms and the Circle Method</i>. Vol. 343, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/978-3-030-86872-7\">10.1007/978-3-030-86872-7</a>.","short":"T.D. Browning, Cubic Forms and the Circle Method, Springer Nature, Cham, 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book","volume":343,"page":"XIV, 166","year":"2021","publication_status":"published","place":"Cham","_id":"10415","intvolume":"       343"},{"date_created":"2021-12-07T10:48:06Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGo"}],"file_date_updated":"2022-03-10T12:10:25Z","title":"Towards designer materials using customizable particle shape","degree_awarded":"MS","abstract":[{"lang":"eng","text":"Those who aim to devise new materials with desirable properties usually examine present methods first. However, they will find out that some approaches can exist only conceptually without high chances to become practically useful. It seems that a numerical technique called automatic differentiation together with increasing supply of computational accelerators will soon shift many methods of the material design from the category ”unimaginable” to the category ”expensive but possible”. Approach we suggest is not an exception. Our overall goal is to have an efficient and generalizable approach allowing to solve inverse design problems. In this thesis we scratch its surface. We consider jammed systems of identical particles. And ask ourselves how the shape of those particles (or the parameters codifying it) may affect mechanical properties of the system. An indispensable part of reaching the answer is an appropriate particle parametrization. We come up with a simple, yet generalizable and purposeful scheme for it. Using our generalizable shape parameterization, we simulate the formation of a solid composed of pentagonal-like particles and measure anisotropy in the resulting elastic response. Through automatic differentiation techniques, we directly connect the shape parameters with the elastic response. Interestingly, for our system we find that less isotropic particles lead to a more isotropic elastic response. Together with other results known about our method it seems that it can be successfully generalized for different inverse design problems."}],"article_processing_charge":"No","date_updated":"2023-09-07T13:34:12Z","alternative_title":["ISTA Master's Thesis"],"doi":"10.15479/at:ista:10422","date_published":"2021-12-07T00:00:00Z","author":[{"id":"865E3C26-AA8C-11E9-A409-C4C4E5697425","full_name":"Piankov, Anton","last_name":"Piankov","first_name":"Anton"}],"has_accepted_license":"1","year":"2021","file":[{"date_updated":"2022-03-10T12:10:25Z","file_id":"10424","file_name":"Thesis.zip","checksum":"114e8f4b2c002c6c352416c12de2c695","file_size":394018,"access_level":"closed","creator":"cchlebak","relation":"source_file","date_created":"2021-12-07T11:13:52Z","content_type":"application/x-zip-compressed"},{"file_name":"Preliminary_pages_Piankov.docx","checksum":"cd15ae991ced352a9959815f794e657c","file_size":47638,"date_updated":"2022-03-10T12:10:25Z","file_id":"10425","date_created":"2021-12-07T11:14:01Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"cchlebak","relation":"source_file"},{"access_level":"open_access","creator":"cchlebak","relation":"main_file","date_created":"2021-12-07T11:20:35Z","success":1,"content_type":"application/pdf","file_id":"10426","date_updated":"2021-12-07T11:20:35Z","checksum":"e6899c798b75ba42fab9822bce309050","file_name":"2021_Piankov_combined.pdf","file_size":484965}],"publication_status":"published","_id":"10422","supervisor":[{"first_name":"Carl Peter","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","month":"12","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2791-4585"]},"citation":{"apa":"Piankov, A. (2021). <i>Towards designer materials using customizable particle shape</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10422\">https://doi.org/10.15479/at:ista:10422</a>","ieee":"A. Piankov, “Towards designer materials using customizable particle shape,” Institute of Science and Technology Austria, 2021.","chicago":"Piankov, Anton. “Towards Designer Materials Using Customizable Particle Shape.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10422\">https://doi.org/10.15479/at:ista:10422</a>.","short":"A. Piankov, Towards Designer Materials Using Customizable Particle Shape, Institute of Science and Technology Austria, 2021.","ista":"Piankov A. 2021. Towards designer materials using customizable particle shape. Institute of Science and Technology Austria.","mla":"Piankov, Anton. <i>Towards Designer Materials Using Customizable Particle Shape</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10422\">10.15479/at:ista:10422</a>.","ama":"Piankov A. Towards designer materials using customizable particle shape. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10422\">10.15479/at:ista:10422</a>"},"ddc":["530"],"day":"07","oa":1,"status":"public"},{"abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently  creates a race condition. This bottleneck  can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the  stochastic gradient descent (SGD) algorithm, which distribute computation  among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be  relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"date_created":"2021-12-08T21:52:28Z","ec_funded":1,"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","title":"On achieving scalability through relaxation","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","mla":"Nadiradze, Giorgi. <i>On Achieving Scalability through Relaxation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10429\">10.15479/at:ista:10429</a>.","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10429\">10.15479/at:ista:10429</a>","apa":"Nadiradze, G. (2021). <i>On achieving scalability through relaxation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10429\">https://doi.org/10.15479/at:ista:10429</a>","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10429\">https://doi.org/10.15479/at:ista:10429</a>.","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021."},"oa":1,"status":"public","has_accepted_license":"1","year":"2021","supervisor":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"_id":"10429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","page":"132","degree_awarded":"PhD","article_processing_charge":"No","doi":"10.15479/at:ista:10429","date_updated":"2023-10-17T11:48:55Z","related_material":{"record":[{"id":"10432","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6673"},{"id":"5965","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10435"}]},"alternative_title":["ISTA Thesis"],"author":[{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","last_name":"Nadiradze","orcid":"0000-0001-5634-0731"}],"date_published":"2021-12-09T00:00:00Z","file_date_updated":"2022-03-28T12:55:12Z","month":"12","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"ddc":["000"],"day":"09","file":[{"access_level":"open_access","creator":"gnadirad","relation":"main_file","date_created":"2021-12-09T17:47:49Z","success":1,"content_type":"application/pdf","date_updated":"2021-12-09T17:47:49Z","file_id":"10436","checksum":"6bf14e9a523387328f016c0689f5e10e","file_name":"Thesis_Final_09_12_2021.pdf","file_size":2370859},{"file_id":"10437","date_updated":"2022-03-28T12:55:12Z","checksum":"914d6c5ca86bd0add471971a8f4c4341","file_name":"Thesis_Final_09_12_2021.zip","file_size":2596924,"creator":"gnadirad","access_level":"closed","relation":"source_file","date_created":"2021-12-09T17:47:49Z","content_type":"application/zip"}],"publication_status":"published"},{"abstract":[{"text":"One key element behind the recent progress of machine learning has been the ability to train machine learning models in large-scale distributed shared-memory and message-passing environments. Most of these models are trained employing variants of stochastic gradient descent (SGD) based optimization, but most methods involve some type of consistency relaxation relative to sequential SGD, to mitigate its large communication or synchronization costs at scale. In this paper, we introduce a general consistency condition covering communication-reduced and asynchronous distributed SGD implementations. Our framework, called elastic consistency, decouples the system-specific aspects of the implementation from the SGD convergence requirements, giving a general way to obtain convergence bounds for a wide variety of distributed SGD methods used in practice. Elastic consistency can be used to re-derive or improve several previous convergence bounds in message-passing and shared-memory settings, but also to analyze new models and distribution schemes. As a direct application, we propose and analyze a new synchronization-avoiding scheduling scheme for distributed SGD, and show that it can be used to efficiently train deep convolutional models for image classification.","lang":"eng"}],"arxiv":1,"ec_funded":1,"date_created":"2021-12-09T09:21:35Z","oa_version":"Published Version","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","title":"Elastic consistency: A practical consistency model for distributed stochastic gradient descent","department":[{"_id":"DaAl"}],"citation":{"ama":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. ; 2021:9037-9045.","ista":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. 2021. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence vol. 35, 9037–9045.","mla":"Nadiradze, Giorgi, et al. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 10, 2021, pp. 9037–45.","short":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the AAAI Conference on Artificial Intelligence, 2021, pp. 9037–9045.","ieee":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Elastic consistency: A practical consistency model for distributed stochastic gradient descent,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 10, pp. 9037–9045.","chicago":"Nadiradze, Giorgi, Ilia Markov, Bapi Chatterjee, Vyacheslav  Kungurtsev, and Dan-Adrian Alistarh. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:9037–45, 2021.","apa":"Nadiradze, G., Markov, I., Chatterjee, B., Kungurtsev, V., &#38; Alistarh, D.-A. (2021). Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 9037–9045). Virtual."},"status":"public","oa":1,"acknowledgement":"We would like to thank Christopher De Sa for his feedback on an earlier draft of this paper, as well as the anonymous AAAI reviewers for their useful comments. This project has received\r\nfunding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Bapi\r\nChatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411 (ISTPlus).","issue":"10","external_id":{"arxiv":["2001.05918"]},"_id":"10432","year":"2021","volume":35,"page":"9037-9045","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"conference","quality_controlled":"1","date_published":"2021-05-18T00:00:00Z","author":[{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","first_name":"Giorgi"},{"full_name":"Markov, Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","first_name":"Ilia","last_name":"Markov"},{"orcid":"0000-0002-2742-4028","last_name":"Chatterjee","first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Bapi"},{"last_name":"Kungurtsev","first_name":"Vyacheslav ","full_name":"Kungurtsev, Vyacheslav "},{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"article_processing_charge":"No","date_updated":"2023-09-07T13:31:39Z","related_material":{"record":[{"id":"10429","relation":"dissertation_contains","status":"public"}]},"conference":{"name":"AAAI: Association for the Advancement of Artificial Intelligence","end_date":"2021-02-09","location":"Virtual","start_date":"2021-02-02"},"month":"05","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"language":[{"iso":"eng"}],"day":"18","intvolume":"        35","main_file_link":[{"url":"https://ojs.aaai.org/index.php/AAAI/article/view/17092","open_access":"1"}],"publication_status":"published"},{"publication":"35th Conference on Neural Information Processing Systems","department":[{"_id":"DaAl"}],"title":"Asynchronous decentralized SGD with quantized and local updates","publisher":"Neural Information Processing Systems Foundation","ec_funded":1,"date_created":"2021-12-09T10:59:12Z","oa_version":"Published Version","arxiv":1,"abstract":[{"lang":"eng","text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"10435","year":"2021","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","status":"public","oa":1,"external_id":{"arxiv":["1910.12308"]},"citation":{"ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: <i>35th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation; 2021.","short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” <i>35th Conference on Neural Information Processing Systems</i>, Neural Information Processing Systems Foundation, 2021.","ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In <i>35th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation, 2021.","ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in <i>35th Conference on Neural Information Processing Systems</i>, Sydney, Australia, 2021.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., &#38; Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In <i>35th Conference on Neural Information Processing Systems</i>. Sydney, Australia: Neural Information Processing Systems Foundation."},"conference":{"end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems","start_date":"2021-12-06","location":"Sydney, Australia"},"author":[{"orcid":"0000-0001-5634-0731","last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi"},{"full_name":"Sabour, Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","first_name":"Amirmojtaba","last_name":"Sabour"},{"first_name":"Peter","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425"},{"full_name":"Li, Shigang","last_name":"Li","first_name":"Shigang"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"}],"date_published":"2021-12-01T00:00:00Z","article_processing_charge":"No","date_updated":"2023-10-17T11:48:56Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"quality_controlled":"1","main_file_link":[{"url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html","open_access":"1"}],"publication_status":"published","day":"01","month":"12","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}]},{"department":[{"_id":"MaSe"}],"title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","publication":"Physical Review Letters","publisher":"American Physical Society","oa_version":"Preprint","date_created":"2021-12-10T07:51:33Z","ec_funded":1,"arxiv":1,"abstract":[{"text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase.","lang":"eng"}],"volume":127,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10527","year":"2021","oa":1,"acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","status":"public","external_id":{"isi":["000923819400004"],"arxiv":["2109.00011"]},"article_type":"original","issue":"24","citation":{"apa":"Ghazaryan, A., Holder, T., Serbyn, M., &#38; Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.247001\">https://doi.org/10.1103/physrevlett.127.247001</a>","ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” <i>Physical Review Letters</i>, vol. 127, no. 24. American Physical Society, 2021.","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.247001\">https://doi.org/10.1103/physrevlett.127.247001</a>.","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” <i>Physical Review Letters</i>, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.247001\">10.1103/physrevlett.127.247001</a>.","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. <i>Physical Review Letters</i>. 2021;127(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.247001\">10.1103/physrevlett.127.247001</a>"},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"article_number":"247001","date_published":"2021-12-09T00:00:00Z","author":[{"orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"},{"full_name":"Holder, Tobias","first_name":"Tobias","last_name":"Holder"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"full_name":"Berg, Erez","first_name":"Erez","last_name":"Berg"}],"date_updated":"2023-08-14T13:19:13Z","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/"}]},"doi":"10.1103/physrevlett.127.247001","article_processing_charge":"No","scopus_import":"1","keyword":["general physics and astronomy"],"quality_controlled":"1","intvolume":"       127","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.00011"}],"publication_status":"published","day":"09","language":[{"iso":"eng"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"month":"12"},{"file_date_updated":"2022-05-16T10:42:22Z","article_number":"e72676","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-12-01T00:00:00Z","author":[{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"full_name":"Lyons, David B","last_name":"Lyons","first_name":"David B"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"article_processing_charge":"No","date_updated":"2023-08-17T06:21:08Z","doi":"10.7554/elife.72676","keyword":["genetics and molecular biology"],"scopus_import":"1","quality_controlled":"1","intvolume":"        10","file":[{"file_id":"11384","date_updated":"2022-05-16T10:42:22Z","file_size":2715200,"file_name":"2021_eLife_Choi.pdf","checksum":"22ed4c55fb550f6da02ae55c359be651","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2022-05-16T10:42:22Z"}],"publication_status":"published","pmid":1,"ddc":["570"],"day":"01","month":"12","isi":1,"project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication":"eLife","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","ec_funded":1,"date_created":"2021-12-10T13:12:08Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin."}],"volume":10,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"10533","year":"2021","has_accepted_license":"1","acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","oa":1,"status":"public","article_type":"original","external_id":{"isi":["000754832000001"],"pmid":["34850679"]},"citation":{"apa":"Choi, J., Lyons, D. B., &#38; Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>","chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>.","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>, vol. 10, e72676, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>"},"publication_identifier":{"issn":["2050-084X"]}},{"file_date_updated":"2021-12-13T09:24:42Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2021-12-07T00:00:00Z","author":[{"first_name":"Jingjin","last_name":"Dong","full_name":"Dong, Jingjin"},{"full_name":"Sami, Selim","last_name":"Sami","first_name":"Selim"},{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs"},{"full_name":"Alessandri, Riccardo","last_name":"Alessandri","first_name":"Riccardo"},{"full_name":"Jahani, Fatimeh","last_name":"Jahani","first_name":"Fatimeh"},{"first_name":"Li","last_name":"Qiu","full_name":"Qiu, Li"},{"first_name":"Siewert J.","last_name":"Marrink","full_name":"Marrink, Siewert J."},{"first_name":"Remco W.A.","last_name":"Havenith","full_name":"Havenith, Remco W.A."},{"full_name":"Hummelen, Jan C.","last_name":"Hummelen","first_name":"Jan C."},{"first_name":"Maria A.","last_name":"Loi","full_name":"Loi, Maria A."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"}],"article_processing_charge":"No","doi":"10.1039/d1tc02753k","date_updated":"2023-08-17T06:18:44Z","scopus_import":"1","quality_controlled":"1","intvolume":"         9","file":[{"relation":"main_file","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","date_created":"2021-12-13T09:24:42Z","success":1,"file_id":"10538","date_updated":"2021-12-13T09:24:42Z","file_size":4979390,"checksum":"6b73c214ce54a6894a5854b4364413d7","file_name":"2021_JMaterChemC_Dong.pdf"}],"publication_status":"published","ddc":["540"],"day":"07","isi":1,"month":"12","language":[{"iso":"eng"}],"publication":"Journal of Materials Chemistry C","title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","department":[{"_id":"MaIb"}],"publisher":"Royal Society of Chemistry","date_created":"2021-12-12T23:01:27Z","oa_version":"Published Version","abstract":[{"text":"For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications.","lang":"eng"}],"volume":9,"page":"16217-16225","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","_id":"10534","year":"2021","has_accepted_license":"1","acknowledgement":"J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983).","oa":1,"status":"public","issue":"45","article_type":"original","external_id":{"isi":["000688135700001"]},"citation":{"ista":"Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.","mla":"Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” <i>Journal of Materials Chemistry C</i>, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:<a href=\"https://doi.org/10.1039/d1tc02753k\">10.1039/d1tc02753k</a>.","short":"J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225.","ama":"Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. <i>Journal of Materials Chemistry C</i>. 2021;9(45):16217-16225. doi:<a href=\"https://doi.org/10.1039/d1tc02753k\">10.1039/d1tc02753k</a>","apa":"Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d1tc02753k\">https://doi.org/10.1039/d1tc02753k</a>","chicago":"Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d1tc02753k\">https://doi.org/10.1039/d1tc02753k</a>.","ieee":"J. Dong <i>et al.</i>, “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” <i>Journal of Materials Chemistry C</i>, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021."},"publication_identifier":{"eissn":["2050-7526"],"issn":["2050-7534"]}},{"article_processing_charge":"No","doi":"10.1371/journal.pcbi.1009661","date_updated":"2022-08-01T10:48:04Z","author":[{"first_name":"Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"date_published":"2021-12-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","article_number":"e1009661","file_date_updated":"2022-05-16T08:53:11Z","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"day":"01","pmid":1,"month":"12","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","success":1,"date_created":"2022-05-16T08:53:11Z","content_type":"application/pdf","file_id":"11383","date_updated":"2022-05-16T08:53:11Z","file_name":"2021_PLOsComBio_Bodova.pdf","checksum":"dcd185d4f7e0acee25edf1d6537f447e","file_size":2299486}],"publication_status":"published","intvolume":"        17","arxiv":1,"abstract":[{"lang":"eng","text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment."}],"publisher":"Public Library of Science","publication":"PLoS Computational Biology","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","date_created":"2021-12-12T23:01:27Z","oa_version":"Published Version","issue":"12","article_type":"original","external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","status":"public","oa":1,"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"citation":{"ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. 2021;17(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>.","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>.","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” <i>PLoS Computational Biology</i>, vol. 17, no. 12. Public Library of Science, 2021.","apa":"Bodova, K., Szep, E., &#38; Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":17,"year":"2021","has_accepted_license":"1","_id":"10535"},{"intvolume":"        11","publication_status":"published","file":[{"date_updated":"2021-12-13T13:32:37Z","file_id":"10539","file_size":9245199,"file_name":"2021_Frontiers_Stefanescu.pdf","checksum":"56cbac80e6891ce750511a30161b7792","relation":"main_file","access_level":"open_access","creator":"alisjak","content_type":"application/pdf","success":1,"date_created":"2021-12-13T13:32:37Z"}],"pmid":1,"day":"18","ddc":["610"],"language":[{"iso":"eng"}],"isi":1,"month":"11","file_date_updated":"2021-12-13T13:32:37Z","article_number":"765151","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Cristina","last_name":"Stefanescu","full_name":"Stefanescu, Cristina"},{"last_name":"Van Gogh","first_name":"Merel","full_name":"Van Gogh, Merel"},{"orcid":"0000-0001-9588-1389","last_name":"Roblek","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","full_name":"Roblek, Marko"},{"full_name":"Heikenwalder, Mathias","last_name":"Heikenwalder","first_name":"Mathias"},{"first_name":"Lubor","last_name":"Borsig","full_name":"Borsig, Lubor"}],"date_published":"2021-11-18T00:00:00Z","doi":"10.3389/fonc.2021.765151","date_updated":"2023-08-17T06:20:32Z","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","volume":11,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10536","year":"2021","has_accepted_license":"1","status":"public","oa":1,"acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","external_id":{"isi":["000726603400001"],"pmid":["34868988"]},"article_type":"original","citation":{"ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. <i>Frontiers in Oncology</i>. 2021;11. doi:<a href=\"https://doi.org/10.3389/fonc.2021.765151\">10.3389/fonc.2021.765151</a>","mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” <i>Frontiers in Oncology</i>, vol. 11, 765151, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fonc.2021.765151\">10.3389/fonc.2021.765151</a>.","ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” <i>Frontiers in Oncology</i>, vol. 11. Frontiers, 2021.","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” <i>Frontiers in Oncology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fonc.2021.765151\">https://doi.org/10.3389/fonc.2021.765151</a>.","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., &#38; Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. <i>Frontiers in Oncology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fonc.2021.765151\">https://doi.org/10.3389/fonc.2021.765151</a>"},"publication_identifier":{"eissn":["2234-943X"]},"title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","department":[{"_id":"DaSi"}],"publication":"Frontiers in Oncology","publisher":"Frontiers","oa_version":"Published Version","date_created":"2021-12-12T23:01:27Z","abstract":[{"lang":"eng","text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner."}]}]