[{"month":"04","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"doi":"10.1063/1.5144759","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1912.02658","open_access":"1"}],"external_id":{"arxiv":["1912.02658"],"isi":["000530448300001"]},"isi":1,"quality_controlled":"1","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"ec_funded":1,"article_number":"164302","author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Xiang","full_name":"Li, Xiang"},{"first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"full_name":"Bighin, Giacomo","first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"first_name":"Richard","last_name":"Schmidt","full_name":"Schmidt, Richard"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8958"}]},"date_updated":"2023-09-07T13:16:42Z","date_created":"2020-09-30T10:33:17Z","volume":152,"acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868.","year":"2020","publication_status":"published","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"publisher":"AIP Publishing","day":"27","article_processing_charge":"No","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"date_published":"2020-04-27T00:00:00Z","publication":"The Journal of Chemical Physics","citation":{"apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., & Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5144759","ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” The Journal of Chemical Physics, vol. 152, no. 16. AIP Publishing, 2020.","ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302.","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 2020;152(16). doi:10.1063/1.5144759","chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/1.5144759.","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” The Journal of Chemical Physics, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:10.1063/1.5144759."},"article_type":"original","abstract":[{"lang":"eng","text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"issue":"16","type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8587","title":"Intermolecular forces and correlations mediated by a phonon bath","status":"public","intvolume":" 152"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level."}],"_id":"8341","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["570"],"title":"In vitro reconstitution of a Rab activation switch","file":[{"access_level":"closed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","file_size":65246782,"content_type":"application/x-zip-compressed","creator":"dernst","relation":"source_file","file_id":"8342","checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z","date_created":"2020-09-08T09:00:29Z"},{"file_name":"2020_Urban_Bezeljak_Thesis.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":31259058,"file_id":"8343","relation":"main_file","date_created":"2020-09-08T09:00:27Z","date_updated":"2021-09-16T12:49:12Z","checksum":"59a62275088b00b7241e6ff4136434c7"}],"oa_version":"Published Version","day":"08","has_accepted_license":"1","article_processing_charge":"No","citation":{"short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria."},"page":"215","date_published":"2020-09-08T00:00:00Z","file_date_updated":"2021-09-16T12:49:12Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2020","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631","first_name":"Urban","last_name":"Bezeljak","full_name":"Bezeljak, Urban"}],"related_material":{"record":[{"id":"7580","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-07T13:17:06Z","date_created":"2020-09-08T08:53:53Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/AT:ISTA:8341","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"degree_awarded":"PhD","language":[{"iso":"eng"}]},{"volume":117,"date_updated":"2023-09-07T13:17:06Z","date_created":"2020-03-12T05:32:26Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/"}],"record":[{"id":"8341","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631","first_name":"Urban","last_name":"Bezeljak"},{"last_name":"Loya","first_name":"Hrushikesh","full_name":"Loya, Hrushikesh"},{"first_name":"Beata M","last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarek, Beata M"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"publication_status":"published","year":"2020","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.1073/pnas.1921027117","project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000521821800040"]},"main_file_link":[{"url":"https://doi.org/10.1101/776567","open_access":"1"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"03","oa_version":"Preprint","intvolume":" 117","status":"public","title":"Stochastic activation and bistability in a Rab GTPase regulatory network","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7580","issue":"12","abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}],"type":"journal_article","date_published":"2020-03-24T00:00:00Z","page":"6504-6549","article_type":"original","citation":{"short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","day":"24","scopus_import":"1"},{"abstract":[{"text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_id":"8034","relation":"main_file","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-26T10:03:58Z","access_level":"open_access","file_name":"Kristof_Huszar-Thesis.pdf","creator":"khuszar","content_type":"application/pdf","file_size":2637562},{"file_name":"Kristof_Huszar-Thesis-source.zip","access_level":"closed","creator":"khuszar","file_size":7163491,"content_type":"application/x-zip-compressed","file_id":"8035","relation":"source_file","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-26T10:10:06Z","checksum":"d5f8456202b32f4a77552ef47a2837d1"}],"oa_version":"Published Version","title":"Combinatorial width parameters for 3-dimensional manifolds","status":"public","ddc":["514"],"_id":"8032","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"26","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-06-26T00:00:00Z","page":"xviii+120","citation":{"ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032."},"file_date_updated":"2020-07-14T12:48:08Z","date_updated":"2023-09-07T13:18:27Z","date_created":"2020-06-26T10:00:36Z","author":[{"full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","first_name":"Kristóf","last_name":"Huszár"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6556"},{"status":"public","relation":"dissertation_contains","id":"7093"}]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","year":"2020","month":"06","publication_identifier":{"isbn":["978-3-99078-006-0"],"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8032","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"day":"14","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-07-14T00:00:00Z","publication":"Computer Aided Verification","citation":{"mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” Computer Aided Verification, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:10.1007/978-3-030-53288-8_14.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In Computer Aided Verification, 12224:275–98. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53288-8_14.","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: Computer Aided Verification. Vol 12224. Springer Nature; 2020:275-298. doi:10.1007/978-3-030-53288-8_14","ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in Computer Aided Verification, 2020, vol. 12224, pp. 275–298.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2020). Refinement for structured concurrent programs. In Computer Aided Verification (Vol. 12224, pp. 275–298). Springer Nature. https://doi.org/10.1007/978-3-030-53288-8_14"},"page":"275-298","abstract":[{"text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Published Version","file":[{"file_name":"2020_LNCS_Kragl.pdf","access_level":"open_access","file_size":804237,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8201","date_updated":"2020-08-06T08:14:54Z","date_created":"2020-08-06T08:14:54Z","success":1}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8195","status":"public","ddc":["000"],"title":"Refinement for structured concurrent programs","intvolume":" 12224","month":"07","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030532871"],"issn":["0302-9743"],"eisbn":["9783030532888"]},"doi":"10.1007/978-3-030-53288-8_14","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000695276000014"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"file_date_updated":"2020-08-06T08:14:54Z","author":[{"first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"8332","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-08-03T11:45:35Z","date_updated":"2023-09-07T13:18:00Z","volume":12224,"acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","year":"2020","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}]},{"oa_version":"Published Version","_id":"8012","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Inductive sequentialization of asynchronous programs","status":"public","abstract":[{"lang":"eng","text":"Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos."}],"type":"conference","date_published":"2020-06-01T00:00:00Z","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","citation":{"mla":"Kragl, Bernhard, et al. “Inductive Sequentialization of Asynchronous Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–42, doi:10.1145/3385412.3385980.","short":"B. Kragl, C. Enea, T.A. Henzinger, S.O. Mutluergil, S. Qadeer, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–242.","chicago":"Kragl, Bernhard, Constantin Enea, Thomas A Henzinger, Suha Orhun Mutluergil, and Shaz Qadeer. “Inductive Sequentialization of Asynchronous Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 227–42. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385980.","ama":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. Inductive sequentialization of asynchronous programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:227-242. doi:10.1145/3385412.3385980","ista":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. 2020. Inductive sequentialization of asynchronous programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 227–242.","apa":"Kragl, B., Enea, C., Henzinger, T. A., Mutluergil, S. O., & Qadeer, S. (2020). Inductive sequentialization of asynchronous programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 227–242). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385980","ieee":"B. Kragl, C. Enea, T. A. Henzinger, S. O. Mutluergil, and S. Qadeer, “Inductive sequentialization of asynchronous programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 227–242."},"page":"227-242","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","first_name":"Bernhard","last_name":"Kragl","full_name":"Kragl, Bernhard"},{"last_name":"Enea","first_name":"Constantin","full_name":"Enea, Constantin"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Mutluergil, Suha Orhun","first_name":"Suha Orhun","last_name":"Mutluergil"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"related_material":{"record":[{"id":"8332","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-06-25T11:40:16Z","date_updated":"2023-09-07T13:18:00Z","year":"2020","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"ToHe"}],"conference":{"end_date":"2020-06-20","start_date":"2020-06-15","location":"London, United Kingdom","name":"PLDI: Programming Language Design and Implementation"},"doi":"10.1145/3385412.3385980","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000614622300016"]},"main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"month":"06","publication_identifier":{"isbn":["9781450376136"]}},{"publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"month":"09","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:8358","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"degree_awarded":"PhD","file_date_updated":"2020-09-11T07:48:10Z","year":"2020","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MaLo"}],"publication_status":"published","related_material":{"record":[{"id":"7572","relation":"dissertation_contains","status":"public"},{"id":"7197","status":"public","relation":"part_of_dissertation"}]},"author":[{"orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R"}],"date_updated":"2023-09-07T13:18:51Z","date_created":"2020-09-10T09:26:49Z","has_accepted_license":"1","article_processing_charge":"No","day":"10","citation":{"short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria."},"page":"135","date_published":"2020-09-10T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n"}],"_id":"8358","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["572"],"title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","file":[{"file_size":141602462,"content_type":"application/pdf","creator":"pcaldas","file_name":"phd_thesis_pcaldas.pdf","access_level":"open_access","date_created":"2020-09-10T12:11:29Z","date_updated":"2020-09-10T12:11:29Z","checksum":"882f93fe9c351962120e2669b84bf088","success":1,"relation":"main_file","file_id":"8364"},{"creator":"pcaldas","file_size":450437458,"content_type":"application/x-zip-compressed","file_name":"phd_thesis_latex_pcaldas.zip","access_level":"closed","date_created":"2020-09-10T12:18:17Z","date_updated":"2020-09-11T07:48:10Z","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_id":"8365","relation":"source_file"}],"oa_version":"Published Version"},{"conference":{"end_date":"2020-09-09","location":"Virtual, Online; Pisa, Italy","start_date":"2020-09-07","name":"ESA: Annual European Symposium on Algorithms"},"doi":"10.4230/LIPIcs.ESA.2020.75","language":[{"iso":"eng"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"month":"08","publication_identifier":{"issn":["18688969"],"isbn":["9783959771627"]},"author":[{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F"},{"full_name":"Rouxel-Labbé, Mael","first_name":"Mael","last_name":"Rouxel-Labbé"},{"full_name":"Teillaud, Monique","first_name":"Monique","last_name":"Teillaud"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9056"}]},"date_created":"2020-10-25T23:01:18Z","date_updated":"2023-09-07T13:29:00Z","volume":173,"year":"2020","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"}],"file_date_updated":"2020-10-27T14:31:52Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","article_number":"75","date_published":"2020-08-26T00:00:00Z","publication":"28th Annual European Symposium on Algorithms","citation":{"chicago":"Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing CGAL Periodic Delaunay Triangulations.” In 28th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.75.","mla":"Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.” 28th Annual European Symposium on Algorithms, vol. 173, 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.75.","short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ista":"Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 75.","apa":"Osang, G. F., Rouxel-Labbé, M., & Teillaud, M. (2020). Generalizing CGAL periodic Delaunay triangulations. In 28th Annual European Symposium on Algorithms (Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.75","ieee":"G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic Delaunay triangulations,” in 28th Annual European Symposium on Algorithms, Virtual, Online; Pisa, Italy, 2020, vol. 173.","ama":"Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay triangulations. In: 28th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.75"},"day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"success":1,"checksum":"fe0f7c49a99ed870c671b911e10d5496","date_updated":"2020-10-27T14:31:52Z","date_created":"2020-10-27T14:31:52Z","file_id":"8712","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":733291,"access_level":"open_access","file_name":"2020_LIPIcs_Osang.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8703","status":"public","ddc":["000"],"title":"Generalizing CGAL periodic Delaunay triangulations","intvolume":" 173","abstract":[{"lang":"eng","text":"Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity. "}],"type":"conference","alternative_title":["LIPIcs"]},{"quality_controlled":"1","oa":1,"citation":{"ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.","ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020.","apa":"Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020."},"publication":"8th International Conference on Learning Representations","language":[{"iso":"eng"}],"date_published":"2020-04-26T00:00:00Z","conference":{"location":"Online","start_date":"2020-04-27","end_date":"2020-04-30","name":"ICLR: International Conference on Learning Representations"},"article_processing_charge":"No","has_accepted_license":"1","month":"04","day":"26","department":[{"_id":"ChLa"}],"status":"public","ddc":["000"],"publication_status":"published","title":"Functional vs. parametric equivalence of ReLU networks","year":"2020","_id":"7481","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"7482","relation":"main_file","checksum":"8d372ea5defd8cb8fdc430111ed754a9","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-11T09:07:27Z","access_level":"open_access","file_name":"main.pdf","creator":"bphuong","content_type":"application/pdf","file_size":405469}],"date_created":"2020-02-11T09:07:37Z","date_updated":"2023-09-07T13:29:50Z","related_material":{"link":[{"relation":"supplementary_material","url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html"}],"record":[{"relation":"dissertation_contains","status":"public","id":"9418"}]},"author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","file_date_updated":"2020-07-14T12:47:59Z","abstract":[{"text":"We address the following question: How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact. Two such transformations are known for feed-forward architectures: permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations. For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling. The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest.","lang":"eng"}]},{"external_id":{"arxiv":["1904.08647 "],"isi":["000546967700022"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"main_file_link":[{"url":"https://arxiv.org/abs/1904.08647","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"doi":"10.1137/19m126284x","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","year":"2020","publication_status":"published","publisher":"Society for Industrial & Applied Mathematics ","department":[{"_id":"RoSe"}],"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"}]},"date_created":"2021-08-06T07:34:16Z","date_updated":"2023-09-07T13:30:11Z","volume":52,"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"SIAM Journal on Mathematical Analysis","citation":{"chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics , 2020. https://doi.org/10.1137/19m126284x.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics , 2020, pp. 605–22, doi:10.1137/19m126284x.","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial & Applied Mathematics , pp. 605–622, 2020.","apa":"Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics . https://doi.org/10.1137/19m126284x","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 2020;52(1):605-622. doi:10.1137/19m126284x"},"article_type":"original","page":"605-622","date_published":"2020-02-12T00:00:00Z","scopus_import":"1","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"day":"12","article_processing_charge":"No","has_accepted_license":"1","_id":"9781","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["510"],"status":"public","title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","intvolume":" 52","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum.","lang":"eng"}],"issue":"1"},{"publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"month":"05","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000511060200001"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00205-019-01486-2","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2020-11-20T09:14:22Z","year":"2020","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10007"}]},"author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"},{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian"}],"volume":236,"date_updated":"2023-09-07T13:30:45Z","date_created":"2020-02-16T23:00:50Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 2020;236:967-1087. doi:10.1007/s00205-019-01486-2","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087.","apa":"Fischer, J. L., & Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01486-2","ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” Archive for Rational Mechanics and Analysis, vol. 236. Springer Nature, pp. 967–1087, 2020.","mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:10.1007/s00205-019-01486-2.","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-019-01486-2."},"publication":"Archive for Rational Mechanics and Analysis","page":"967-1087","article_type":"original","date_published":"2020-05-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7489","intvolume":" 236","status":"public","ddc":["530","532"],"title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","file":[{"relation":"main_file","file_id":"8779","date_updated":"2020-11-20T09:14:22Z","date_created":"2020-11-20T09:14:22Z","checksum":"f107e21b58f5930876f47144be37cf6c","success":1,"file_name":"2020_ArchRatMechAn_Fischer.pdf","access_level":"open_access","file_size":1897571,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.05478"}],"citation":{"chicago":"Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, n.d.","mla":"Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, 2003.05478.","short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).","ista":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.","apa":"Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.","ieee":"J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” arXiv. .","ama":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv."},"oa":1,"external_id":{"arxiv":["2003.05478"]},"publication":"arXiv","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-03-11T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"11","month":"03","_id":"10012","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385.","year":"2020","department":[{"_id":"JuFi"}],"status":"public","publication_status":"submitted","title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","related_material":{"record":[{"id":"10007","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","last_name":"Hensel"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"},{"full_name":"Simon, Thilo","first_name":"Thilo","last_name":"Simon"}],"oa_version":"Preprint","date_updated":"2023-09-07T13:30:45Z","date_created":"2021-09-13T12:17:11Z","type":"preprint","article_number":"2003.05478","ec_funded":1,"abstract":[{"text":"We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a \"gradient flow calibration\" ensures that the route of steepest descent in the energy landscape is unique and stable.","lang":"eng"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8755","status":"public","title":"Surpassing the resistance quantum with a geometric superinductor","ddc":["530"],"intvolume":" 14","oa_version":"Published Version","file":[{"date_updated":"2021-03-29T11:43:20Z","date_created":"2021-03-29T11:43:20Z","checksum":"2a634abe75251ae7628cd54c8a4ce2e8","success":1,"relation":"main_file","file_id":"9300","content_type":"application/pdf","file_size":2607823,"creator":"dernst","file_name":"2020_PhysReviewApplied_Peruzzo.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. "}],"issue":"4","publication":"Physical Review Applied","citation":{"short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","mla":"Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:10.1103/PhysRevApplied.14.044055.","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied. American Physical Society, 2020. https://doi.org/10.1103/PhysRevApplied.14.044055.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 2020;14(4). doi:10.1103/PhysRevApplied.14.044055","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” Physical Review Applied, vol. 14, no. 4. American Physical Society, 2020.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.14.044055","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055."},"article_type":"original","date_published":"2020-10-29T00:00:00Z","scopus_import":"1","day":"29","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). ","year":"2020","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","author":[{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea"},{"first_name":"Farid","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13070"},{"id":"9920","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-11-15T23:01:17Z","date_updated":"2023-09-07T13:31:22Z","volume":14,"article_number":"044055","file_date_updated":"2021-03-29T11:43:20Z","ec_funded":1,"external_id":{"isi":["000582797300003"],"arxiv":["2007.01644"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"}],"doi":"10.1103/PhysRevApplied.14.044055","acknowledged_ssus":[{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["23317019"]}},{"oa_version":"Preprint","_id":"7573","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 139","title":"Homogenisation of one-dimensional discrete optimal transport","status":"public","issue":"7","abstract":[{"lang":"eng","text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport."}],"type":"journal_article","date_published":"2020-07-01T00:00:00Z","citation":{"short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:10.1016/j.matpur.2020.02.008.","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees. Elsevier, 2020. https://doi.org/10.1016/j.matpur.2020.02.008.","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","apa":"Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234."},"publication":"Journal de Mathematiques Pures et Appliquees","page":"204-234","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","related_material":{"record":[{"id":"10030","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Gladbach, Peter","first_name":"Peter","last_name":"Gladbach"},{"first_name":"Eva","last_name":"Kopfer","full_name":"Kopfer, Eva"},{"full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"}],"volume":139,"date_created":"2020-03-08T23:00:47Z","date_updated":"2023-09-07T13:31:05Z","year":"2020","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","department":[{"_id":"JaMa"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"doi":"10.1016/j.matpur.2020.02.008","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1905.05757"],"isi":["000539439400008"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.05757"}],"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["00217824"]},"month":"07"},{"date_created":"2021-09-17T10:57:27Z","date_updated":"2023-09-07T13:31:05Z","oa_version":"Preprint","author":[{"full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","last_name":"Forkert"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo"}],"related_material":{"record":[{"id":"11739","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"10030"}]},"status":"public","publication_status":"submitted","title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","department":[{"_id":"JaMa"}],"_id":"10022","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.","year":"2020","abstract":[{"text":"We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.","lang":"eng"}],"ec_funded":1,"article_number":"2008.10962","type":"preprint","language":[{"iso":"eng"}],"date_published":"2020-08-25T00:00:00Z","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"page":"33","publication":"arXiv","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.10962"}],"external_id":{"arxiv":["2008.10962"]},"citation":{"ama":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","ista":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. .","apa":"Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","mla":"Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962.","short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d."},"oa":1,"day":"25","month":"08","article_processing_charge":"No"},{"scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No","publication":"Proceedings of the 37th International Conference on Machine Learning","citation":{"ista":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.","apa":"Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press.","ieee":"N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in Proceedings of the 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5416–5425.","ama":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.","chicago":"Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In Proceedings of the 37th International Conference on Machine Learning, 119:5416–25. ML Research Press, 2020.","mla":"Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25.","short":"N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425."},"page":"5416-5425","date_published":"2020-07-12T00:00:00Z","type":"conference","abstract":[{"text":"We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. ","lang":"eng"}],"_id":"8724","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"On the sample complexity of adversarial multi-source PAC learning","ddc":["000"],"status":"public","intvolume":" 119","file":[{"file_size":281286,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_PMLR_Konstantinov.pdf","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","success":1,"date_updated":"2021-02-15T09:00:01Z","date_created":"2021-02-15T09:00:01Z","relation":"main_file","file_id":"9120"}],"oa_version":"Published Version","month":"07","publication_identifier":{"issn":["2640-3498"]},"oa":1,"external_id":{"arxiv":["2002.10384"]},"quality_controlled":"1","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"conference":{"end_date":"2020-07-18","location":"Online","start_date":"2020-07-12","name":"ICML: International Conference on Machine Learning"},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-02-15T09:00:01Z","ec_funded":1,"year":"2020","acknowledgement":"Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H"},{"full_name":"Frantar, Elias","last_name":"Frantar","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"id":"10799","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"supplementary_material","url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf"}]},"date_created":"2020-11-05T15:25:58Z","date_updated":"2023-09-07T13:42:08Z","volume":119},{"doi":"10.1088/1367-2630/abae44","language":[{"iso":"eng"}],"external_id":{"isi":["000573298000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"25681","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","name":"Analytic and machine learning approaches to composite quantum impurities"},{"name":"A path-integral approach to composite impurities","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"}],"month":"09","publication_identifier":{"issn":["13672630"]},"author":[{"last_name":"Rzadkowski","first_name":"Wojciech","orcid":"0000-0002-1106-4419","id":"48C55298-F248-11E8-B48F-1D18A9856A87","full_name":"Rzadkowski, Wojciech"},{"full_name":"Defenu, N","last_name":"Defenu","first_name":"N"},{"first_name":"S","last_name":"Chiacchiera","full_name":"Chiacchiera, S"},{"full_name":"Trombettoni, A","last_name":"Trombettoni","first_name":"A"},{"last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10759"}]},"date_created":"2020-10-11T22:01:14Z","date_updated":"2023-09-07T13:44:16Z","volume":22,"acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","year":"2020","publication_status":"published","publisher":"IOP Publishing","department":[{"_id":"MiLe"}],"file_date_updated":"2020-10-12T12:18:47Z","ec_funded":1,"article_number":"093026","date_published":"2020-09-01T00:00:00Z","publication":"New Journal of Physics","citation":{"chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44.","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44.","ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020.","apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44"},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"success":1,"checksum":"c9238fff422e7a957c3a0d559f756b3a","date_updated":"2020-10-12T12:18:47Z","date_created":"2020-10-12T12:18:47Z","file_id":"8650","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":2725143,"access_level":"open_access","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8644","title":"Detecting composite orders in layered models via machine learning","ddc":["530"],"status":"public","intvolume":" 22","abstract":[{"text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures.","lang":"eng"}],"issue":"9","type":"journal_article"},{"volume":21,"date_updated":"2023-09-07T13:43:51Z","date_created":"2020-10-25T23:01:19Z","related_material":{"record":[{"id":"11473","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2020","acknowledgement":"Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria)","ec_funded":1,"file_date_updated":"2020-10-27T12:49:04Z","language":[{"iso":"eng"}],"doi":"10.1007/s00023-020-00969-3","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2003.12371"],"isi":["000578111800002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["1424-0637"]},"month":"12","file":[{"creator":"cziletti","file_size":469831,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Annales_Mysliwy.pdf","success":1,"checksum":"c12c9c1e6f08def245e42f3cb1d83827","date_updated":"2020-10-27T12:49:04Z","date_created":"2020-10-27T12:49:04Z","file_id":"8711","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 21","title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","ddc":["530"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8705","issue":"12","abstract":[{"text":"We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model.","lang":"eng"}],"type":"journal_article","date_published":"2020-12-01T00:00:00Z","page":"4003-4025","article_type":"original","citation":{"short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","mla":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3.","chicago":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3.","ama":"Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3","apa":"Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3","ieee":"K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” Annales Henri Poincare, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020.","ista":"Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025."},"publication":"Annales Henri Poincare","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1"},{"article_number":"e1007642","file_date_updated":"2020-07-14T12:48:00Z","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2020","date_updated":"2023-09-12T11:02:24Z","date_created":"2020-03-06T07:39:38Z","volume":16,"author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"related_material":{"record":[{"id":"9716","relation":"research_data","status":"deleted"},{"id":"9776","status":"public","relation":"research_data"},{"relation":"used_in_publication","status":"public","id":"9779"},{"status":"public","relation":"dissertation_contains","id":"8155"},{"status":"public","relation":"research_data","id":"9777"}]},"month":"02","publication_identifier":{"issn":["1553-7358"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000526725200019"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1007642","type":"journal_article","abstract":[{"text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.","lang":"eng"}],"issue":"2","ddc":["000","570"],"title":"The relation between crosstalk and gene regulation form revisited","status":"public","intvolume":" 16","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7569","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2209325,"content_type":"application/pdf","file_name":"2020_PlosCompBio_Grah.pdf","access_level":"open_access","date_created":"2020-03-09T15:12:21Z","date_updated":"2020-07-14T12:48:00Z","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","file_id":"7579","relation":"main_file"}],"scopus_import":"1","day":"25","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"PLOS Computational Biology","citation":{"ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.","apa":"Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.","mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020)."},"date_published":"2020-02-25T00:00:00Z"},{"article_processing_charge":"No","month":"11","day":"05","date_published":"2020-11-05T00:00:00Z","doi":"10.1101/2020.11.03.366948","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.03.366948"}],"citation":{"mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948.","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948"},"external_id":{"pmid":["PPR234457 "]},"oa":1,"publication":"bioRxiv","abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"type":"preprint","author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"full_name":"Halbritter, Florian","last_name":"Halbritter","first_name":"Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"full_name":"Suzuki, Toru","last_name":"Suzuki","first_name":"Toru"},{"full_name":"Asami, Maki","first_name":"Maki","last_name":"Asami"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"last_name":"Ma","first_name":"Xiaoyan","full_name":"Ma, Xiaoyan"},{"last_name":"Lackner","first_name":"Andreas","full_name":"Lackner, Andreas"},{"last_name":"Warr","first_name":"Nick","full_name":"Warr, Nick"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","first_name":"Andreas","last_name":"Beyer"},{"full_name":"Perry, Anthony C. F.","last_name":"Perry","first_name":"Anthony C. F."},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"}],"oa_version":"Preprint","date_created":"2020-11-26T07:17:19Z","date_updated":"2023-09-12T11:05:28Z","pmid":1,"year":"2020","_id":"8813","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"SiHi"}],"publication_status":"submitted","status":"public","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent"},{"main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}],"citation":{"ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002","apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002.","short":"R. Grah, T. Friedlander, (2020).","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002."},"oa":1,"doi":"10.1371/journal.pcbi.1007642.s002","date_published":"2020-02-25T00:00:00Z","article_processing_charge":"No","day":"25","month":"02","_id":"9777","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","status":"public","title":"Maximizing crosstalk","related_material":{"record":[{"id":"7569","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"oa_version":"None","date_created":"2021-08-06T07:21:51Z","date_updated":"2023-09-12T11:02:25Z","type":"research_data_reference"},{"oa_version":"Published Version","file":[{"creator":"bkragl","content_type":"application/pdf","file_size":1348815,"access_level":"open_access","file_name":"kragl-thesis.pdf","checksum":"26fe261550f691280bda4c454bf015c7","date_created":"2020-09-04T12:17:47Z","date_updated":"2020-09-04T12:17:47Z","file_id":"8333","relation":"main_file"},{"file_name":"kragl-thesis.zip","access_level":"closed","file_size":372312,"content_type":"application/zip","creator":"bkragl","relation":"source_file","file_id":"8335","date_updated":"2020-09-04T13:00:17Z","date_created":"2020-09-04T13:00:17Z","checksum":"b9694ce092b7c55557122adba8337ebc"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8332","status":"public","ddc":["000"],"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-03T00:00:00Z","citation":{"chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332"},"page":"120","article_processing_charge":"No","has_accepted_license":"1","day":"03","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"133"},{"id":"8012","status":"public","relation":"part_of_dissertation"},{"id":"8195","relation":"part_of_dissertation","status":"public"},{"id":"160","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Kragl","first_name":"Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard"}],"date_updated":"2023-09-13T08:45:08Z","date_created":"2020-09-04T12:24:12Z","year":"2020","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2020-09-04T13:00:17Z","doi":"10.15479/AT:ISTA:8332","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"09"},{"publist_id":"7983","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"JaMa"}],"publication_status":"published","year":"2020","volume":52,"date_updated":"2023-09-18T08:13:15Z","date_created":"2018-12-11T11:44:28Z","author":[{"full_name":"Gladbach, Peter","last_name":"Gladbach","first_name":"Peter"},{"last_name":"Kopfer","first_name":"Eva","full_name":"Kopfer, Eva"},{"full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"month":"10","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01092"}],"external_id":{"arxiv":["1809.01092"],"isi":["000546975100017"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/19M1243440","type":"journal_article","issue":"3","abstract":[{"text":"We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric.","lang":"eng"}],"intvolume":" 52","title":"Scaling limits of discrete optimal transport","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"71","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"2759-2802","article_type":"original","citation":{"chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802.","mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.","apa":"Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440","ieee":"P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020.","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.","ama":"Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440"},"publication":"SIAM Journal on Mathematical Analysis","date_published":"2020-10-01T00:00:00Z"},{"publication":"IEEE Transactions on Visualization and Computer Graphics","citation":{"chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628","ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.","ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302.","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628"},"article_type":"original","page":"2288-2302","date_published":"2020-06-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"5681","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Simulating liquids on dynamically warping grids","ddc":["006"],"status":"public","intvolume":" 26","file":[{"relation":"main_file","file_id":"8626","checksum":"8d4c55443a0ee335bb5bb652de503042","success":1,"date_updated":"2020-10-08T08:34:53Z","date_created":"2020-10-08T08:34:53Z","access_level":"open_access","file_name":"preprint.pdf","file_size":21910098,"content_type":"application/pdf","creator":"wojtan"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.","lang":"eng"}],"issue":"6","external_id":{"pmid":["30507534"],"isi":["000532295600014"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1109/TVCG.2018.2883628","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["10772626"],"eissn":["19410506"]},"acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"IEEE","author":[{"first_name":"Ibayashi","last_name":"Hikaru","full_name":"Hikaru, Ibayashi"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"date_created":"2018-12-16T22:59:21Z","date_updated":"2023-09-18T09:30:01Z","volume":26,"file_date_updated":"2020-10-08T08:34:53Z"},{"abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8967","checksum":"3994c54a1241451d561db1d4f43bad30","success":1,"date_created":"2020-12-22T10:55:56Z","date_updated":"2020-12-22T10:55:56Z","access_level":"open_access","file_name":"THESIS_Xiang_Li.pdf","content_type":"application/pdf","file_size":3622305,"creator":"xli"},{"checksum":"0954ecfc5554c05615c14de803341f00","date_updated":"2020-12-30T07:18:03Z","date_created":"2020-12-22T10:56:03Z","relation":"source_file","file_id":"8968","file_size":4018859,"content_type":"application/x-zip-compressed","creator":"xli","access_level":"closed","file_name":"THESIS_Xiang_Li.zip"}],"status":"public","title":"Rotation of coupled cold molecules in the presence of a many-body environment","ddc":["539"],"_id":"8958","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","has_accepted_license":"1","day":"21","date_published":"2020-12-21T00:00:00Z","page":"125","citation":{"chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958"},"ec_funded":1,"file_date_updated":"2020-12-30T07:18:03Z","date_updated":"2023-09-20T11:30:58Z","date_created":"2020-12-21T09:44:30Z","related_material":{"record":[{"id":"5886","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8587"},{"id":"1120","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang","last_name":"Li","full_name":"Li, Xiang"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2020","publication_identifier":{"issn":["2663-337X"]},"month":"12","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8958","project":[{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"oa":1},{"ddc":["003"],"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","status":"public","_id":"8386","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"date_updated":"2020-09-14T12:18:43Z","date_created":"2020-09-14T01:02:59Z","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","relation":"source_file","file_id":"8388","content_type":"application/x-zip-compressed","file_size":1245800191,"creator":"rzhang","file_name":"Thesis_Ran.zip","access_level":"closed"},{"success":1,"checksum":"817e20c33be9247f906925517c56a40d","date_created":"2020-09-15T12:51:53Z","date_updated":"2020-09-15T12:51:53Z","file_id":"8396","relation":"main_file","creator":"rzhang","content_type":"application/pdf","file_size":161385316,"access_level":"open_access","file_name":"PhD_thesis_Ran Zhang_20200915.pdf"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.","lang":"eng"}],"page":"148","citation":{"ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386."},"date_published":"2020-09-14T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"14","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","year":"2020","date_updated":"2023-09-22T09:49:31Z","date_created":"2020-09-14T01:04:53Z","related_material":{"record":[{"id":"486","status":"public","relation":"part_of_dissertation"},{"id":"1002","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","first_name":"Ran"}],"ec_funded":1,"file_date_updated":"2020-09-15T12:51:53Z","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.15479/AT:ISTA:8386","publication_identifier":{"issn":["2663-337X"]},"month":"09"},{"day":"22","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-06-22T00:00:00Z","citation":{"mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020."},"page":"178","abstract":[{"text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/x-zip-compressed","file_size":392794743,"creator":"dernst","access_level":"closed","file_name":"JK_thesis_latex_source_files.zip","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","date_created":"2020-06-22T09:22:04Z","date_updated":"2020-07-14T12:48:07Z","relation":"main_file","file_id":"7997"},{"checksum":"1de716bf110dbd77d383e479232bf496","date_created":"2020-06-22T09:21:29Z","date_updated":"2020-07-14T12:48:07Z","file_id":"7998","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":28453247,"access_level":"open_access","file_name":"PhD_thesis_JK_pdfa.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7996","status":"public","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","ddc":["530"],"month":"06","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:7996","supervisor":[{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:48:07Z","author":[{"first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1328"},{"id":"7541","relation":"part_of_dissertation","status":"public"},{"id":"77","relation":"part_of_dissertation","status":"public"},{"id":"23","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"840"}]},"date_updated":"2023-09-26T15:50:22Z","date_created":"2020-06-22T09:22:23Z","year":"2020","publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.","lang":"eng"}],"_id":"8272","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 12225","ddc":["000"],"title":"Stochastic games with lexicographic reachability-safety objectives","status":"public","file":[{"creator":"dernst","content_type":"application/pdf","file_size":625056,"access_level":"open_access","file_name":"2020_LNCS_CAV_Chatterjee.pdf","success":1,"checksum":"093d4788d7d5b2ce0ffe64fbe7820043","date_created":"2020-08-17T11:32:44Z","date_updated":"2020-08-17T11:32:44Z","file_id":"8276","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14","citation":{"chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21"},"publication":"International Conference on Computer Aided Verification","page":"398-420","date_published":"2020-07-14T00:00:00Z","ec_funded":1,"file_date_updated":"2020-08-17T11:32:44Z","year":"2020","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"id":"12738","relation":"later_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P","last_name":"Katoen"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"},{"last_name":"Winkler","first_name":"Tobias","full_name":"Winkler, Tobias"}],"volume":12225,"date_updated":"2023-10-03T11:36:13Z","date_created":"2020-08-16T22:00:58Z","publication_identifier":{"isbn":["9783030532901"],"eissn":["16113349"],"issn":["03029743"]},"month":"07","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000695272500021"],"arxiv":["2005.04018"]},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","isi":1,"doi":"10.1007/978-3-030-53291-8_21","conference":{"name":"CAV: Computer Aided Verification"},"language":[{"iso":"eng"}]},{"scopus_import":"1","article_processing_charge":"No","day":"27","page":"145-161","citation":{"ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006."},"publication":"Methods in Cell Biology","date_published":"2020-02-27T00:00:00Z","alternative_title":["Methods in Cell Biology"],"type":"book_chapter","abstract":[{"text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material.","lang":"eng"}],"intvolume":" 158","title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7572","oa_version":"Preprint","publication_identifier":{"issn":["0091679X"]},"month":"02","project":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000611826500008"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"language":[{"iso":"eng"}],"doi":"10.1016/bs.mcb.2020.01.006","ec_funded":1,"department":[{"_id":"MaLo"}],"publisher":"Elsevier","editor":[{"full_name":"Tran, Phong ","first_name":"Phong ","last_name":"Tran"}],"publication_status":"published","year":"2020","volume":158,"date_updated":"2023-10-04T09:50:24Z","date_created":"2020-03-08T23:00:47Z","related_material":{"record":[{"id":"8358","relation":"part_of_dissertation","status":"public"}]},"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R"},{"full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}]},{"external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"}],"doi":"10.1038/s41564-019-0657-5","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["2058-5276"]},"year":"2020","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","pmid":1,"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Springer Nature","author":[{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","first_name":"Natalia S.","last_name":"Baranova"},{"first_name":"Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"last_name":"Hernández-Rocamora","first_name":"Víctor M.","full_name":"Hernández-Rocamora, Víctor M."},{"full_name":"Alfonso, Carlos","first_name":"Carlos","last_name":"Alfonso"},{"full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Germán","last_name":"Rivas","full_name":"Rivas, Germán"},{"last_name":"Vollmer","first_name":"Waldemar","full_name":"Vollmer, Waldemar"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"related_material":{"record":[{"id":"14280","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release","description":"News on IST Homepage"}]},"date_updated":"2023-10-06T12:22:38Z","date_created":"2020-01-28T16:14:41Z","volume":5,"ec_funded":1,"publication":"Nature Microbiology","citation":{"mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020."},"article_type":"letter_note","page":"407-417","date_published":"2020-01-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7387","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","status":"public","intvolume":" 5","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}]},{"doi":"10.1556/012.2020.57.2.1454","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000570978400005"]},"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0081-6906"],"eissn":["1588-2896"]},"month":"07","author":[{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","first_name":"Mathijs"}],"volume":57,"date_updated":"2023-10-10T13:05:27Z","date_created":"2020-07-24T07:09:18Z","year":"2020","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","publisher":"Akadémiai Kiadó","department":[{"_id":"HeEd"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-24T07:09:06Z","date_published":"2020-07-24T00:00:00Z","citation":{"ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454."},"publication":"Studia Scientiarum Mathematicarum Hungarica","page":"193-199","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2020-07-24T07:09:06Z","date_updated":"2020-07-24T07:09:06Z","file_id":"8164","relation":"main_file","creator":"mwintrae","file_size":1476072,"content_type":"application/pdf","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8163","intvolume":" 57","title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","status":"public","ddc":["510"],"issue":"2","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"type":"journal_article"},{"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"117-128","publication":"Iranian Journal of Mathematical Sciences and Informatics","citation":{"ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128."},"date_published":"2020-10-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. ","lang":"eng"}],"issue":"2","title":"A note on belief structures and s-approximation spaces","ddc":["000"],"status":"public","intvolume":" 15","_id":"8671","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_size":261688,"content_type":"application/pdf","creator":"dernst","file_name":"2020_ijmsi_Shakiba_accepted.pdf","access_level":"open_access","date_created":"2020-10-19T11:14:20Z","date_updated":"2020-10-19T11:14:20Z","checksum":"f299661a6d51cda6d255a76be696f48d","success":1,"relation":"main_file","file_id":"8676"}],"month":"10","publication_identifier":{"eissn":["2008-9473"],"issn":["1735-4463"]},"quality_controlled":"1","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"oa":1,"external_id":{"arxiv":["1805.10672"]},"language":[{"iso":"eng"}],"doi":"10.29252/ijmsi.15.2.117","file_date_updated":"2020-10-19T11:14:20Z","publication_status":"published","publisher":"Iranian Academic Center for Education, Culture and Research","department":[{"_id":"KrCh"}],"acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","year":"2020","date_created":"2020-10-18T22:01:36Z","date_updated":"2023-10-16T09:25:00Z","volume":15,"author":[{"full_name":"Shakiba, A.","last_name":"Shakiba","first_name":"A."},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Hooshmandasl, M.R.","last_name":"Hooshmandasl","first_name":"M.R."},{"full_name":"Alambardar Meybodi, M.","last_name":"Alambardar Meybodi","first_name":"M."}]},{"type":"journal_article","abstract":[{"text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.","lang":"eng"}],"intvolume":" 25","title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","status":"public","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6359","file":[{"checksum":"8e7c42e72596f6889d786e8e8b89994f","success":1,"date_updated":"2020-09-21T13:15:02Z","date_created":"2020-09-21T13:15:02Z","relation":"main_file","file_id":"8549","file_size":273042,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_EJournProbab_Dareiotis.pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"16","article_type":"original","citation":{"ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP479","ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479","mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479.","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479."},"publication":"Electronic Journal of Probability","date_published":"2020-07-16T00:00:00Z","article_number":"82","file_date_updated":"2020-09-21T13:15:02Z","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JaMa"}],"publication_status":"published","year":"2020","volume":25,"date_created":"2019-04-30T07:40:17Z","date_updated":"2023-10-16T09:22:50Z","author":[{"full_name":"Dareiotis, Konstantinos","last_name":"Dareiotis","first_name":"Konstantinos"},{"full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser"}],"publication_identifier":{"eissn":["1083-6489"]},"month":"07","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000550150700001"],"arxiv":["1812.04583"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/20-EJP479"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8390","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","status":"public","ddc":["000"],"file":[{"date_created":"2020-09-14T13:39:14Z","date_updated":"2020-09-14T13:39:14Z","success":1,"checksum":"c914d2f88846032f3d8507734861b6ee","file_id":"8391","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":30224591,"file_name":"2020_Thesis_Royer.pdf","access_level":"open_access"},{"creator":"dernst","file_size":74227627,"content_type":"application/x-zip-compressed","file_name":"thesis_sources.zip","access_level":"closed","date_created":"2020-09-14T13:39:17Z","date_updated":"2020-09-14T13:39:17Z","checksum":"ae98fb35d912cff84a89035ae5794d3c","file_id":"8392","relation":"main_file"}],"oa_version":"Published Version","day":"14","has_accepted_license":"1","article_processing_charge":"No","citation":{"mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390"},"page":"197","date_published":"2020-09-14T00:00:00Z","file_date_updated":"2020-09-14T13:39:17Z","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","year":"2020","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"}],"author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer","first_name":"Amélie"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7936"},{"id":"7937","relation":"part_of_dissertation","status":"public"},{"id":"8193","status":"public","relation":"part_of_dissertation"},{"id":"8092","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"911"}]},"date_created":"2020-09-14T13:42:09Z","date_updated":"2023-10-16T10:04:02Z","month":"09","publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/AT:ISTA:8390","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"degree_awarded":"PhD","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"conference":{"start_date":"2020-06-14","location":"Virtual","end_date":"2020-06-19","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"doi":"10.1109/CVPR42600.2020.00752","quality_controlled":"1","external_id":{"arxiv":["2004.04180"]},"main_file_link":[{"open_access":"1","url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf"}],"oa":1,"month":"07","publication_identifier":{"eissn":["2575-7075"],"eisbn":["9781728171685"]},"date_created":"2020-07-31T16:53:49Z","date_updated":"2023-10-17T07:37:11Z","author":[{"full_name":"Henderson, Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","first_name":"Paul M","last_name":"Henderson"},{"full_name":"Tsiminaki, Vagia","first_name":"Vagia","last_name":"Tsiminaki"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"IEEE","year":"2020","file_date_updated":"2020-07-31T16:57:12Z","date_published":"2020-07-01T00:00:00Z","page":"7498-7507","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","citation":{"ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507.","apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752.","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507."},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","file":[{"file_size":10262773,"content_type":"application/pdf","creator":"phenders","file_name":"paper.pdf","access_level":"open_access","date_updated":"2020-07-31T16:57:12Z","date_created":"2020-07-31T16:57:12Z","success":1,"relation":"main_file","file_id":"8187"}],"title":"Leveraging 2D data to learn textured 3D mesh generation","status":"public","ddc":["004"],"_id":"8186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes.","lang":"eng"}],"type":"conference"},{"article_number":"1687175","author":[{"full_name":"Sinclair, Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4566-0593","first_name":"Scott A","last_name":"Sinclair"},{"full_name":"Krämer, U.","first_name":"U.","last_name":"Krämer"}],"date_updated":"2023-10-17T09:01:48Z","date_created":"2020-01-30T10:12:04Z","volume":15,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Taylor & Francis","month":"01","publication_identifier":{"issn":["1559-2324"]},"doi":"10.1080/15592324.2019.1687175","language":[{"iso":"eng"}],"external_id":{"pmid":["31696764"],"isi":["000494909300001"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements."}],"issue":"1","type":"journal_article","oa_version":"Submitted Version","_id":"7416","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","status":"public","intvolume":" 15","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-01-01T00:00:00Z","publication":"Plant Signaling & Behavior","citation":{"mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175, Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175.","short":"S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis, 2020. https://doi.org/10.1080/15592324.2019.1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 15(1), 1687175.","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.","apa":"Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2019.1687175"},"article_type":"original"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"quality_controlled":"1","isi":1,"project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445"}],"doi":"10.1371/journal.ppat.1008277","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["1553-7374"]},"year":"2020","pmid":1,"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"FlSc"}],"author":[{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"full_name":"Morado, Dustin R.","first_name":"Dustin R.","last_name":"Morado"},{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089","first_name":"Vladyslav","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav"},{"first_name":"Clifton L.","last_name":"Ricana","full_name":"Ricana, Clifton L."},{"full_name":"Lyddon, Terri D.","last_name":"Lyddon","first_name":"Terri D."},{"full_name":"Broad, Arianna M.","first_name":"Arianna M.","last_name":"Broad"},{"full_name":"Feathers, J. Ryan","last_name":"Feathers","first_name":"J. Ryan"},{"first_name":"Marc C.","last_name":"Johnson","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"last_name":"Perilla","first_name":"Juan R.","full_name":"Perilla, Juan R."},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"related_material":{"record":[{"id":"9723","status":"deleted","relation":"research_data"}]},"date_updated":"2023-10-17T12:29:34Z","date_created":"2020-02-06T18:47:17Z","volume":16,"article_number":"e1008277","file_date_updated":"2020-07-14T12:47:59Z","publication":"PLOS Pathogens","citation":{"chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277"},"article_type":"original","date_published":"2020-01-27T00:00:00Z","scopus_import":"1","day":"27","has_accepted_license":"1","article_processing_charge":"No","_id":"7464","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","ddc":["570"],"status":"public","intvolume":" 16","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":4551246,"creator":"dernst","file_name":"2020_PLOSPatho_Dick.pdf","access_level":"open_access","date_created":"2020-02-11T10:07:28Z","date_updated":"2020-07-14T12:47:59Z","checksum":"a297f54d1fef0efe4789ca00f37f241e","relation":"main_file","file_id":"7484"}],"type":"journal_article","abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"issue":"1"},{"day":"17","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2020-01-17T00:00:00Z","publication":"PLoS computational biology","citation":{"ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494","mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494."},"article_type":"original","abstract":[{"text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"7441","date_created":"2020-02-03T07:32:42Z","date_updated":"2020-07-14T12:47:53Z","checksum":"ce32ee2d2f53aed832f78bbd47e882df","file_name":"2020_PlosCompBio_Tkadlec.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1817531,"creator":"dernst"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7212","ddc":["000"],"status":"public","title":"Limits on amplifiers of natural selection under death-Birth updating","intvolume":" 16","month":"01","publication_identifier":{"eissn":["15537358"]},"doi":"10.1371/journal.pcbi.1007494","language":[{"iso":"eng"}],"external_id":{"isi":["000510916500025"],"arxiv":["1906.02785"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"article_number":"e1007494","author":[{"first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"}]},"date_updated":"2023-10-17T12:29:47Z","date_created":"2019-12-23T13:45:11Z","volume":16,"year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science"},{"date_published":"2020-01-12T00:00:00Z","citation":{"ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196."},"page":"144","has_accepted_license":"1","article_processing_charge":"No","day":"12","file":[{"file_id":"7255","relation":"source_file","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-12T11:49:49Z","access_level":"closed","file_name":"thesis.zip","creator":"jtkadlec","file_size":21100497,"content_type":"application/zip"},{"content_type":"application/pdf","file_size":11670983,"creator":"dernst","access_level":"open_access","file_name":"2020_Tkadlec_Thesis.pdf","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","date_created":"2020-01-28T07:32:42Z","date_updated":"2020-07-14T12:47:52Z","relation":"main_file","file_id":"7367"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7196","title":"A role of graphs in evolutionary processes","status":"public","ddc":["519"],"abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:7196","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"}],"oa":1,"publication_identifier":{"eissn":["2663-337X"]},"month":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7210"},{"relation":"dissertation_contains","status":"public","id":"5751"},{"id":"7212","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"}],"date_created":"2019-12-20T12:26:36Z","date_updated":"2023-10-17T12:29:46Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:52Z"},{"citation":{"apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84."},"publication":"Proceedings of the 37th International Conference on Machine Learning","page":"8773-8784","date_published":"2020-07-13T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"13","_id":"9198","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 119","ddc":["000"],"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","status":"public","oa_version":"Published Version","file":[{"checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","success":1,"date_updated":"2021-03-02T15:38:14Z","date_created":"2021-03-02T15:38:14Z","relation":"main_file","file_id":"9217","file_size":5336380,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_PMLR_Shevchenko.pdf"}],"type":"conference","abstract":[{"lang":"eng","text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks."}],"external_id":{"arxiv":["1912.10095"]},"oa":1,"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","language":[{"iso":"eng"}],"month":"07","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","year":"2020","department":[{"_id":"MaMo"}],"publisher":"ML Research Press","publication_status":"published","author":[{"last_name":"Shevchenko","first_name":"Alexander","full_name":"Shevchenko, Alexander"},{"first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"volume":119,"date_created":"2021-02-25T09:36:22Z","date_updated":"2023-10-17T12:43:19Z","file_date_updated":"2021-03-02T15:38:14Z"},{"date_published":"2020-06-20T00:00:00Z","article_type":"original","page":"51-67","publication":"Computational and Mathematical Biophysics","citation":{"ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100."},"day":"20","has_accepted_license":"1","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"9171","date_created":"2021-02-19T13:56:24Z","date_updated":"2021-02-19T13:56:24Z","checksum":"cea41de9937d07a3b927d71ee8b4e432","success":1,"file_name":"2020_CompMathBiophysics_Akopyan2.pdf","access_level":"open_access","file_size":562359,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","title":"The weighted mean curvature derivative of a space-filling diagram","status":"public","ddc":["510"],"intvolume":" 8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9157","abstract":[{"text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy.","lang":"eng"}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1515/cmb-2020-0100","quality_controlled":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","publication_identifier":{"issn":["2544-7297"]},"date_created":"2021-02-17T15:13:01Z","date_updated":"2023-10-17T12:34:51Z","volume":8,"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"De Gruyter","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","file_date_updated":"2021-02-19T13:56:24Z","ec_funded":1},{"file_date_updated":"2021-02-19T13:33:19Z","ec_funded":1,"author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"date_created":"2021-02-17T15:12:44Z","date_updated":"2023-10-17T12:35:10Z","volume":8,"acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","publication_status":"published","publisher":"De Gruyter","department":[{"_id":"HeEd"}],"month":"07","publication_identifier":{"issn":["2544-7297"]},"doi":"10.1515/cmb-2020-0101","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1908.06777"]},"oa":1,"quality_controlled":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9170","checksum":"ca43a7440834eab6bbea29c59b56ef3a","success":1,"date_updated":"2021-02-19T13:33:19Z","date_created":"2021-02-19T13:33:19Z","access_level":"open_access","file_name":"2020_CompMathBiophysics_Akopyan.pdf","file_size":707452,"content_type":"application/pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9156","ddc":["510"],"status":"public","title":"The weighted Gaussian curvature derivative of a space-filling diagram","intvolume":" 8","day":"21","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-07-21T00:00:00Z","publication":"Computational and Mathematical Biophysics","citation":{"short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88."},"article_type":"original","page":"74-88"},{"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":" Institute of Mathematical Statistics","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","year":"2020","date_updated":"2023-10-17T12:51:56Z","date_created":"2020-12-27T23:01:17Z","volume":25,"author":[{"full_name":"Redig, Frank","first_name":"Frank","last_name":"Redig"},{"first_name":"Ellen","last_name":"Saada","full_name":"Saada, Ellen"},{"id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico","last_name":"Sau","full_name":"Sau, Federico"}],"article_number":"138","file_date_updated":"2020-12-28T08:24:08Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"oa":1,"external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"language":[{"iso":"eng"}],"doi":"10.1214/20-EJP536","month":"10","publication_identifier":{"eissn":["1083-6489"]},"ddc":["510"],"title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","status":"public","intvolume":" 25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8973","file":[{"relation":"main_file","file_id":"8976","checksum":"d75359b9814e78d57c0a481b7cde3751","success":1,"date_updated":"2020-12-28T08:24:08Z","date_created":"2020-12-28T08:24:08Z","access_level":"open_access","file_name":"2020_ElectronJProbab_Redig.pdf","file_size":696653,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity.","lang":"eng"}],"article_type":"original","publication":"Electronic Journal of Probability","citation":{"ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536."},"date_published":"2020-10-21T00:00:00Z","scopus_import":"1","day":"21","has_accepted_license":"1","article_processing_charge":"No"},{"oa_version":"Preprint","_id":"179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 169","title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","status":"public","issue":"16","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.","lang":"eng"}],"type":"journal_article","date_published":"2020-09-10T00:00:00Z","citation":{"chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal. Duke University Press, 2020. https://doi.org/10.1215/00127094-2020-0031.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031.","short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","apa":"Browning, T. D., & Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2020-0031","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” Duke Mathematical Journal, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 2020;169(16):3099-3165. doi:10.1215/00127094-2020-0031"},"publication":"Duke Mathematical Journal","page":"3099-3165","article_type":"original","article_processing_charge":"No","day":"10","author":[{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","full_name":"Browning, Timothy D"},{"full_name":"Heath Brown, Roger","first_name":"Roger","last_name":"Heath Brown"}],"volume":169,"date_created":"2018-12-11T11:45:02Z","date_updated":"2023-10-17T12:51:10Z","year":"2020","publisher":"Duke University Press","department":[{"_id":"TiBr"}],"publication_status":"published","doi":"10.1215/00127094-2020-0031","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000582676300002"],"arxiv":["1805.10715"]},"main_file_link":[{"url":"https://arxiv.org/abs/1805.10715","open_access":"1"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0012-7094"]},"month":"09"},{"author":[{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"198"}]},"date_created":"2021-08-06T13:09:57Z","date_updated":"2023-10-18T06:36:00Z","oa_version":"Published Version","_id":"9814","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","status":"public","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","publisher":"Royal Society","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners"}],"type":"research_data_reference","doi":"10.6084/m9.figshare.5973013.v1","date_published":"2020-10-15T00:00:00Z","citation":{"ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, 10.6084/m9.figshare.5973013.v1.","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1","mla":"Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"oa":1,"month":"10","day":"15","article_processing_charge":"No"},{"month":"07","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/PhysRevLett.125.043202","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1912.10218","open_access":"1"}],"external_id":{"isi":["000552227400008"],"pmid":["32794788"],"arxiv":["1912.10218"]},"oa":1,"quality_controlled":"1","isi":1,"article_number":"043202","author":[{"first_name":"Benjamin K.","last_name":"Malia","full_name":"Malia, Benjamin K."},{"first_name":"Julián","last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián"},{"full_name":"Wu, Yunfan","last_name":"Wu","first_name":"Yunfan"},{"full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten"},{"last_name":"Kasevich","first_name":"Mark A.","full_name":"Kasevich, Mark A."}],"date_updated":"2023-10-18T08:38:35Z","date_created":"2020-08-24T06:24:04Z","volume":125,"acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"OnHo"}],"publisher":"American Physical Society","day":"24","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-24T00:00:00Z","publication":"Physical Review Letters","citation":{"ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202."},"article_type":"original","abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"issue":"4","type":"journal_article","oa_version":"Preprint","_id":"8285","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","intvolume":" 125"},{"language":[{"iso":"eng"}],"conference":{"start_date":"2020-12-06","location":"Vancouver, Canada","end_date":"2020-12-12","name":"NeurIPS: Conference on Neural Information Processing Systems"},"project":[{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z"},{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html"}],"publication_identifier":{"issn":["1049-5258"]},"month":"12","volume":33,"date_created":"2021-07-04T22:01:27Z","date_updated":"2023-10-18T09:20:55Z","related_material":{"link":[{"url":"https://doi.org/10.1101/2020.10.24.353409","relation":"is_continued_by"}],"record":[{"relation":"dissertation_contains","status":"public","id":"14422"}]},"author":[{"last_name":"Confavreux","first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"},{"first_name":"Everton J.","last_name":"Agnes","full_name":"Agnes, Everton J."},{"full_name":"Lillicrap, Timothy","first_name":"Timothy","last_name":"Lillicrap"},{"first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"department":[{"_id":"TiVo"}],"publication_status":"published","year":"2020","acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris.","ec_funded":1,"date_published":"2020-12-06T00:00:00Z","page":"16398-16408","citation":{"ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020."},"publication":"Advances in Neural Information Processing Systems","article_processing_charge":"No","day":"06","scopus_import":"1","oa_version":"Published Version","intvolume":" 33","title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","status":"public","_id":"9633","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"type":"conference"},{"publication_identifier":{"eissn":["22111247"]},"month":"12","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1016/j.celrep.2020.108463","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Long Term Fellowship","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["33264621"],"isi":["000595658100018"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"ec_funded":1,"file_date_updated":"2020-12-14T07:33:39Z","article_number":"108463","volume":33,"date_created":"2020-12-13T23:01:21Z","date_updated":"2023-11-16T13:03:31Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/plants-on-aspirin/","description":"News on IST Homepage","relation":"press_release"}]},"author":[{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous"},{"full_name":"Zhang, Xixi","first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627"},{"full_name":"Klíma, Petr","first_name":"Petr","last_name":"Klíma"},{"first_name":"Jie","last_name":"Liu","full_name":"Liu, Jie"},{"last_name":"Bailly","first_name":"Aurélien","full_name":"Bailly, Aurélien"},{"full_name":"Ferro, Noel","first_name":"Noel","last_name":"Ferro"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2020","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","date_published":"2020-12-01T00:00:00Z","article_type":"original","citation":{"chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463.","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","ieee":"S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020.","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463"},"publication":"Cell Reports","issue":"9","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2020_CellReports_Tan.pdf","creator":"dernst","file_size":8056434,"content_type":"application/pdf","file_id":"8948","relation":"main_file","success":1,"checksum":"ed18cba0fb48ed2e789381a54cc21904","date_updated":"2020-12-14T07:33:39Z","date_created":"2020-12-14T07:33:39Z"}],"oa_version":"Published Version","intvolume":" 33","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","ddc":["580"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"8943"},{"date_updated":"2023-11-30T10:55:13Z","date_created":"2020-06-07T22:00:51Z","volume":117,"author":[{"full_name":"Xu, Duo","last_name":"Xu","first_name":"Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"full_name":"Ma, Xingyu","last_name":"Ma","first_name":"Xingyu","orcid":"0000-0002-0179-9737","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"id":"14530","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"National Academy of Sciences","year":"2020","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1913716117","isi":1,"quality_controlled":"1","project":[{"grant_number":"I04188","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","call_identifier":"FWF"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"main_file_link":[{"url":"https://arxiv.org/abs/2005.11190","open_access":"1"}],"external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"]},"oa":1,"month":"05","publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"oa_version":"Preprint","status":"public","title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","intvolume":" 117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7932","abstract":[{"text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer.","lang":"eng"}],"issue":"21","type":"journal_article","date_published":"2020-05-26T00:00:00Z","article_type":"original","page":"11233-11239","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117.","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117","ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239."},"day":"26","article_processing_charge":"No","scopus_import":"1"},{"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6183"}]},"date_updated":"2023-12-18T10:46:09Z","date_created":"2023-12-18T10:37:43Z","volume":25,"year":"2020","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"EMS Press","file_date_updated":"2023-12-18T10:42:32Z","doi":"10.4171/dm/780","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1804.07752"]},"quality_controlled":"1","month":"09","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"oa_version":"Published Version","file":[{"file_id":"14695","relation":"main_file","success":1,"checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","date_created":"2023-12-18T10:42:32Z","date_updated":"2023-12-18T10:42:32Z","access_level":"open_access","file_name":"2020_DocumentaMathematica_Alt.pdf","creator":"dernst","content_type":"application/pdf","file_size":1374708}],"_id":"14694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","status":"public","intvolume":" 25","abstract":[{"lang":"eng","text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases."}],"type":"journal_article","date_published":"2020-09-01T00:00:00Z","publication":"Documenta Mathematica","citation":{"mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780","ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780"},"article_type":"original","page":"1421-1539","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["General Mathematics"]}]