[{"publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"language":[{"iso":"eng"}],"volume":15,"issue":"1","abstract":[{"lang":"eng","text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development."}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154","open_access":"1"}],"scopus_import":"1","intvolume":" 15","month":"01","date_updated":"2023-09-06T15:23:04Z","department":[{"_id":"JiFr"}],"_id":"7417","type":"journal_article","article_type":"original","status":"public","year":"2020","isi":1,"publication":"Plant Signaling & Behavior","day":"01","date_created":"2020-01-30T10:14:14Z","doi":"10.1080/15592324.2019.1687185","date_published":"2020-01-01T00:00:00Z","oa":1,"publisher":"Informa UK Limited","quality_controlled":"1","citation":{"chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior. Informa UK Limited, 2020. https://doi.org/10.1080/15592324.2019.1687185.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 15(1), e1687185.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” Plant Signaling & Behavior, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:10.1080/15592324.2019.1687185.","ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687185","apa":"Sinclair, S. A., Gille, S., Pauly, M., & Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling & Behavior. Informa UK Limited. https://doi.org/10.1080/15592324.2019.1687185","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” Plant Signaling & Behavior, vol. 15, no. 1. Informa UK Limited, 2020.","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling & Behavior 15 (2020)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","last_name":"Sinclair","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A"},{"first_name":"S.","full_name":"Gille, S.","last_name":"Gille"},{"last_name":"Pauly","full_name":"Pauly, M.","first_name":"M."},{"last_name":"Krämer","full_name":"Krämer, U.","first_name":"U."}],"title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","article_number":"e1687185"},{"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-11-18T11:14:37Z","file_name":"2020_CommMathPhysics_Erdoes.pdf","date_updated":"2020-11-18T11:14:37Z","file_size":2904574,"creator":"dernst","file_id":"8771","checksum":"c3a683e2afdcea27afa6880b01e53dc2","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"volume":378,"abstract":[{"text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 378","month":"09","date_updated":"2023-09-07T12:54:12Z","ddc":["530","510"],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-11-18T11:14:37Z","_id":"6185","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","year":"2020","has_accepted_license":"1","isi":1,"publication":"Communications in Mathematical Physics","day":"01","page":"1203-1278","date_created":"2019-03-28T10:21:15Z","doi":"10.1007/s00220-019-03657-4","date_published":"2020-09-01T00:00:00Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","citation":{"mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:10.1007/s00220-019-03657-4.","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” Communications in Mathematical Physics, vol. 378. Springer Nature, pp. 1203–1278, 2020.","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278.","apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03657-4","ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 2020;378:1203-1278. doi:10.1007/s00220-019-03657-4","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03657-4.","ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1809.03971"],"isi":["000529483000001"]},"author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"supervisor":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"date_updated":"2023-09-07T13:03:12Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:48:01Z","_id":"7629","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","creator":"dernst","date_updated":"2020-07-14T12:48:01Z","file_size":3297129,"date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_PDFA.pdf"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","file_id":"7658","file_size":1063908,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"Thesis_Forkert_source.zip","date_created":"2020-04-14T10:47:59Z"}],"language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","citation":{"chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Forkert","full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L"}],"article_processing_charge":"No","title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"has_accepted_license":"1","year":"2020","day":"31","page":"154","doi":"10.15479/AT:ISTA:7629","date_published":"2020-03-31T00:00:00Z","date_created":"2020-04-02T06:40:23Z","publisher":"Institute of Science and Technology Austria","oa":1},{"article_processing_charge":"No","author":[{"full_name":"Szep, Eniko","last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"}],"title":"Local adaptation in metapopulations","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"158","date_created":"2020-09-28T07:33:38Z","doi":"10.15479/AT:ISTA:8574","date_published":"2020-09-20T00:00:00Z","year":"2020","has_accepted_license":"1","day":"20","type":"dissertation","status":"public","_id":"8574","department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-28T07:25:37Z","date_updated":"2023-09-07T13:11:39Z","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"oa_version":"Published Version","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","success":1,"date_updated":"2020-09-28T07:25:35Z","file_size":6354833,"creator":"dernst","date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"8576","checksum":"a8de2c14a1bb4e53c857787efbb289e1","file_size":23020401,"date_updated":"2020-09-28T07:25:37Z","creator":"dernst","file_name":"thesisFiles_EnikoSzep.zip","date_created":"2020-09-28T07:25:37Z"}]},{"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7524"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:59Z","file_size":1563429,"creator":"dernst","date_created":"2020-02-24T09:15:06Z","file_name":"thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7515","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6"},{"date_created":"2020-02-24T09:15:16Z","file_name":"thesis_source.zip","date_updated":"2020-07-14T12:47:59Z","file_size":2028038,"creator":"dernst","file_id":"7516","checksum":"ad7425867b52d7d9e72296e87bc9cb67","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"7514","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:59Z","ddc":["510"],"date_updated":"2023-09-07T13:12:42Z","supervisor":[{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2020-02-24T09:17:27Z","doi":"10.15479/AT:ISTA:7514","date_published":"2020-02-24T00:00:00Z","page":"148","day":"24","year":"2020","has_accepted_license":"1","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"The free energy of a dilute two-dimensional Bose gas","article_processing_charge":"No","author":[{"full_name":"Mayer, Simon","last_name":"Mayer","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514."}},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","page":"191","date_created":"2020-09-09T14:27:01Z","date_published":"2020-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:8353","year":"2020","has_accepted_license":"1","day":"09","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}],"article_processing_charge":"No","author":[{"last_name":"Steiner","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"}],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","citation":{"ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353.","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"oa_version":"None","related_material":{"record":[{"status":"public","id":"8284","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8354","checksum":"2388d7e6e7a4d364c096fa89f305c3de","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-09T14:22:35Z","file_name":"Thesis_Julia_Steiner_pdfA.pdf","creator":"jsteiner","date_updated":"2021-09-16T12:40:56Z","file_size":117547589},{"file_name":"Thesis_Julia_Steiner.docx","date_created":"2020-09-09T14:23:25Z","creator":"jsteiner","file_size":223328668,"date_updated":"2020-09-15T08:48:37Z","file_id":"8355","checksum":"ba112f957b7145462d0ab79044873ee9","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"type":"dissertation","status":"public","_id":"8353","file_date_updated":"2021-09-16T12:40:56Z","department":[{"_id":"LeSa"}],"date_updated":"2023-09-07T13:14:09Z","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"ddc":["572"]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589."},"title":"Novel insights into PIN polarity regulation during Arabidopsis development","author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin"}],"article_processing_charge":"No","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","publisher":"Institute of Science and Technology Austria","oa":1,"day":"30","has_accepted_license":"1","year":"2020","date_published":"2020-09-30T00:00:00Z","doi":"10.15479/AT:ISTA:8589","date_created":"2020-09-30T14:50:51Z","page":"164","_id":"8589","status":"public","type":"dissertation","ddc":["580"],"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"date_updated":"2023-09-07T13:13:05Z","file_date_updated":"2021-10-01T13:33:02Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"09","alternative_title":["ISTA Thesis"],"file":[{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"c4bda1947d4c09c428ac9ce667b02327","file_id":"8590","creator":"dernst","date_updated":"2020-09-30T14:50:20Z","file_size":49198118,"date_created":"2020-09-30T14:50:20Z","file_name":"2020_Han_Thesis.docx"},{"file_size":15513963,"date_updated":"2021-10-01T13:33:02Z","creator":"dernst","file_name":"2020_Han_Thesis.pdf","date_created":"2020-09-30T14:49:59Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","file_id":"8591"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"7643","status":"public"}]}},{"date_updated":"2023-09-07T13:14:08Z","ddc":["570"],"file_date_updated":"2020-08-24T13:31:53Z","department":[{"_id":"LeSa"}],"_id":"8284","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-08-24T13:31:53Z","file_name":"2020_eLife_Steiner.pdf","date_updated":"2020-08-24T13:31:53Z","file_size":7320493,"creator":"cziletti","file_id":"8289","checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8353","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}]},"volume":9,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 9","month":"07","citation":{"mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020.","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407","apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407.","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["32735215"],"isi":["000562123600001"]},"article_processing_charge":"No","author":[{"first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia","last_name":"Steiner"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","article_number":"e59407","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","grant_number":"24741"}],"year":"2020","has_accepted_license":"1","isi":1,"publication":"eLife","day":"31","date_created":"2020-08-24T06:24:04Z","date_published":"2020-07-31T00:00:00Z","doi":"10.7554/eLife.59407","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1"},{"year":"2020","has_accepted_license":"1","day":"24","page":"310","date_created":"2020-07-23T09:51:28Z","doi":"10.15479/AT:ISTA:8155","date_published":"2020-07-24T00:00:00Z","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok"}],"title":"Gene regulation across scales – how biophysical constraints shape evolution","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8176","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","date_updated":"2020-07-27T12:00:07Z","file_size":16638998,"creator":"rgrah"},{"access_level":"closed","relation":"main_file","content_type":"application/zip","file_id":"8177","creator":"rgrah","date_updated":"2020-07-30T13:04:55Z","file_size":347459978,"date_created":"2020-07-27T12:02:23Z","file_name":"Thesis_new.zip"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7675","status":"public"},{"status":"public","id":"7569","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7652"}]},"abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07","date_updated":"2023-09-07T13:13:27Z","supervisor":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"ddc":["530","570"],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z","_id":"8155","type":"dissertation","status":"public"},{"title":"SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism","author":[{"last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","full_name":"Rakusova, Hana","last_name":"Rakusova"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["32107280"],"isi":["000536641800018"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212.","ieee":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism,” Plant Physiology, vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.","short":"H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology 183 (2020) 37–40.","ama":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40. doi:10.1104/pp.20.00212","apa":"Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020). SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212","chicago":"Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml. “SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.” Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.","ista":"Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism. Plant Physiology. 183(5), 37–40."},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"doi":"10.1104/pp.20.00212","date_published":"2020-05-08T00:00:00Z","date_created":"2020-04-06T10:06:40Z","page":"37-40","day":"08","publication":"Plant Physiology","isi":1,"year":"2020","quality_controlled":"1","publisher":"American Society of Plant Biologists","oa":1,"acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship). ","department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T13:13:04Z","status":"public","article_type":"letter_note","type":"journal_article","_id":"7643","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8589"}]},"volume":183,"issue":"5","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"publication_status":"published","month":"05","intvolume":" 183","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.20.00212"}],"oa_version":"Published Version","pmid":1},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","month":"04","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.","lang":"eng"}],"oa_version":"Preprint","date_created":"2020-04-23T10:12:51Z","related_material":{"record":[{"status":"public","id":"8155","relation":"dissertation_contains"}]},"date_published":"2020-04-09T00:00:00Z","doi":"10.1101/2020.04.08.029405","publication_status":"published","year":"2020","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"09","type":"preprint","project":[{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"status":"public","_id":"7675","article_processing_charge":"No","author":[{"orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Normative models of enhancer function","date_updated":"2023-09-07T13:13:26Z","citation":{"chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” BioRxiv. Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.04.08.029405.","ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, 10.1101/2020.04.08.029405.","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.08.029405.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer function. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.04.08.029405","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv. 2020. doi:10.1101/2020.04.08.029405","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” bioRxiv. Cold Spring Harbor Laboratory, 2020.","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"The hole system of triangulated shapes","article_processing_charge":"No","author":[{"first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck","full_name":"Ölsböck, Katharina","orcid":"0000-0002-4672-8297"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020."},"date_created":"2020-02-06T14:56:53Z","doi":"10.15479/AT:ISTA:7460","date_published":"2020-02-10T00:00:00Z","page":"155","day":"10","year":"2020","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:58Z","ddc":["514"],"date_updated":"2023-09-07T13:15:30Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","_id":"7460","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6608"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","file_id":"7461","date_updated":"2020-07-14T12:47:58Z","file_size":76195184,"creator":"koelsboe","date_created":"2020-02-06T14:43:54Z","file_name":"thesis_ist-final_noack.pdf"},{"file_name":"latex-files.zip","date_created":"2020-02-06T14:52:45Z","file_size":122103715,"date_updated":"2020-07-14T12:47:58Z","creator":"koelsboe","checksum":"7a52383c812b0be64d3826546509e5a4","file_id":"7462","description":"latex source files, figures","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}]},{"author":[{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"}],"article_processing_charge":"No","title":"On the average-case hardness of total search problems","citation":{"mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"page":"126","doi":"10.15479/AT:ISTA:7896","date_published":"2020-05-25T00:00:00Z","date_created":"2020-05-26T14:08:55Z","has_accepted_license":"1","year":"2020","day":"25","publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:04Z","supervisor":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_updated":"2023-09-07T13:15:55Z","ddc":["000"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7896","related_material":{"record":[{"relation":"part_of_dissertation","id":"6677","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_name":"2020_Thesis_Kamath.pdf","date_created":"2020-05-26T14:08:13Z","file_size":1622742,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst","file_id":"7897","checksum":"b39e2e1c376f5819b823fb7077491c64","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"date_created":"2020-05-26T14:08:23Z","file_name":"Thesis_Kamath.zip","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","file_size":15301529,"checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","file_id":"7898","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"oa_version":"Published Version"},{"publisher":"IEEE","quality_controlled":"1","oa":1,"date_published":"2020-03-01T00:00:00Z","doi":"10.1109/WACV45572.2020.9093288","date_created":"2020-06-07T22:00:53Z","year":"2020","day":"01","publication":"IEEE Winter Conference on Applications of Computer Vision","article_number":"1716-1725","author":[{"orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer","first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2004.12623"]},"title":"Localizing grouped instances for efficient detection in low-resource scenarios","citation":{"ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093288.","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","apa":"Royer, A., & Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093288","ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093288","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” IEEE Winter Conference on Applications of Computer Vision, 1716–1725, IEEE, 2020, doi:10.1109/WACV45572.2020.9093288."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/2004.12623","open_access":"1"}],"month":"03","abstract":[{"text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"8390"}]},"publication_identifier":{"isbn":["9781728165530"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2020-03-01","location":" Snowmass Village, CO, United States","end_date":"2020-03-05"},"status":"public","_id":"7936","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:17Z"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/2008.11995"}],"month":"03","abstract":[{"text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"id":"8331","status":"deleted","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"8390"}]},"publication_identifier":{"isbn":["9781728165530"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2020-03-01","location":"Snowmass Village, CO, United States","end_date":"2020-03-05"},"status":"public","_id":"7937","department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:17Z","publisher":"IEEE","quality_controlled":"1","oa":1,"doi":"10.1109/WACV45572.2020.9093635","date_published":"2020-03-01T00:00:00Z","date_created":"2020-06-07T22:00:53Z","year":"2020","day":"01","publication":"2020 IEEE Winter Conference on Applications of Computer Vision","article_number":"2180-2189","author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"external_id":{"arxiv":["2008.11995"]},"article_processing_charge":"No","title":"A flexible selection scheme for minimum-effort transfer learning","citation":{"mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” 2020 IEEE Winter Conference on Applications of Computer Vision, 2180–2189, IEEE, 2020, doi:10.1109/WACV45572.2020.9093635.","apa":"Royer, A., & Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In 2020 IEEE Winter Conference on Applications of Computer Vision. Snowmass Village, CO, United States: IEEE. https://doi.org/10.1109/WACV45572.2020.9093635","ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE; 2020. doi:10.1109/WACV45572.2020.9093635","ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in 2020 IEEE Winter Conference on Applications of Computer Vision, Snowmass Village, CO, United States, 2020.","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In 2020 IEEE Winter Conference on Applications of Computer Vision. IEEE, 2020. https://doi.org/10.1109/WACV45572.2020.9093635.","ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"related_material":{"record":[{"id":"8331","status":"deleted","relation":"dissertation_contains"},{"id":"8390","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783030306717"]},"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.05139"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.","lang":"eng"}],"department":[{"_id":"ChLa"}],"date_updated":"2023-09-07T13:16:18Z","status":"public","type":"book_chapter","_id":"8092","date_created":"2020-07-05T22:00:46Z","date_published":"2020-01-08T00:00:00Z","doi":"10.1007/978-3-030-30671-7_3","page":"33-49","publication":"Domain Adaptation for Visual Understanding","day":"08","year":"2020","oa":1,"quality_controlled":"1","publisher":"Springer Nature","title":"XGAN: Unsupervised image-to-image translation for many-to-many mappings","editor":[{"full_name":"Singh, Richa","last_name":"Singh","first_name":"Richa"},{"last_name":"Vatsa","full_name":"Vatsa, Mayank","first_name":"Mayank"},{"last_name":"Patel","full_name":"Patel, Vishal M.","first_name":"Vishal M."},{"last_name":"Ratha","full_name":"Ratha, Nalini","first_name":"Nalini"}],"external_id":{"arxiv":["1711.05139"]},"article_processing_charge":"No","author":[{"first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer"},{"first_name":"Konstantinos","full_name":"Bousmalis, Konstantinos","last_name":"Bousmalis"},{"first_name":"Stephan","full_name":"Gouws, Stephan","last_name":"Gouws"},{"last_name":"Bertsch","full_name":"Bertsch, Fred","first_name":"Fred"},{"first_name":"Inbar","full_name":"Mosseri, Inbar","last_name":"Mosseri"},{"first_name":"Forrester","last_name":"Cole","full_name":"Cole, Forrester"},{"full_name":"Murphy, Kevin","last_name":"Murphy","first_name":"Kevin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Royer, Amélie, et al. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” Domain Adaptation for Visual Understanding, edited by Richa Singh et al., Springer Nature, 2020, pp. 33–49, doi:10.1007/978-3-030-30671-7_3.","apa":"Royer, A., Bousmalis, K., Gouws, S., Bertsch, F., Mosseri, I., Cole, F., & Murphy, K. (2020). XGAN: Unsupervised image-to-image translation for many-to-many mappings. In R. Singh, M. Vatsa, V. M. Patel, & N. Ratha (Eds.), Domain Adaptation for Visual Understanding (pp. 33–49). Springer Nature. https://doi.org/10.1007/978-3-030-30671-7_3","ama":"Royer A, Bousmalis K, Gouws S, et al. XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Singh R, Vatsa M, Patel VM, Ratha N, eds. Domain Adaptation for Visual Understanding. Springer Nature; 2020:33-49. doi:10.1007/978-3-030-30671-7_3","short":"A. Royer, K. Bousmalis, S. Gouws, F. Bertsch, I. Mosseri, F. Cole, K. Murphy, in:, R. Singh, M. Vatsa, V.M. Patel, N. Ratha (Eds.), Domain Adaptation for Visual Understanding, Springer Nature, 2020, pp. 33–49.","ieee":"A. Royer et al., “XGAN: Unsupervised image-to-image translation for many-to-many mappings,” in Domain Adaptation for Visual Understanding, R. Singh, M. Vatsa, V. M. Patel, and N. Ratha, Eds. Springer Nature, 2020, pp. 33–49.","chicago":"Royer, Amélie, Konstantinos Bousmalis, Stephan Gouws, Fred Bertsch, Inbar Mosseri, Forrester Cole, and Kevin Murphy. “XGAN: Unsupervised Image-to-Image Translation for Many-to-Many Mappings.” In Domain Adaptation for Visual Understanding, edited by Richa Singh, Mayank Vatsa, Vishal M. Patel, and Nalini Ratha, 33–49. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-30671-7_3.","ista":"Royer A, Bousmalis K, Gouws S, Bertsch F, Mosseri I, Cole F, Murphy K. 2020.XGAN: Unsupervised image-to-image translation for many-to-many mappings. In: Domain Adaptation for Visual Understanding. , 33–49."}},{"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-sa/4.0/","related_material":{"record":[{"status":"public","id":"7950","relation":"part_of_dissertation"},{"id":"5986","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":13661779,"date_updated":"2020-07-14T12:48:05Z","creator":"zmasarov","file_name":"THESIS_Zuzka_Masarova.pdf","date_created":"2020-06-08T00:34:00Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_id":"7945"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"45341a35b8f5529c74010b7af43ac188","file_id":"7946","date_updated":"2020-07-14T12:48:05Z","file_size":32184006,"creator":"zmasarov","date_created":"2020-06-08T00:35:30Z","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip"}],"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"dissertation","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"status":"public","_id":"7944","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:05Z","date_updated":"2023-09-07T13:17:37Z","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["516","514"],"oa":1,"publisher":"Institute of Science and Technology Austria","page":"160","date_created":"2020-06-08T00:49:46Z","doi":"10.15479/AT:ISTA:7944","date_published":"2020-06-09T00:00:00Z","year":"2020","has_accepted_license":"1","day":"09","article_processing_charge":"No","author":[{"full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"}],"title":"Reconfiguration problems","citation":{"mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"department":[{"_id":"MiLe"},{"_id":"RoSe"}],"date_updated":"2023-09-07T13:16:42Z","article_type":"original","type":"journal_article","status":"public","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"_id":"8587","volume":152,"related_material":{"record":[{"relation":"dissertation_contains","id":"8958","status":"public"}]},"issue":"16","ec_funded":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"month":"04","intvolume":" 152","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."}],"oa_version":"Preprint","author":[{"last_name":"Li","full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang"},{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","last_name":"Deuchert","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1912.02658"],"isi":["000530448300001"]},"title":"Intermolecular forces and correlations mediated by a phonon bath","citation":{"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.","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.","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"},{"name":"A path-integral approach to composite impurities","grant_number":"M02641","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"article_number":"164302","doi":"10.1063/1.5144759","date_published":"2020-04-27T00:00:00Z","date_created":"2020-09-30T10:33:17Z","isi":1,"year":"2020","day":"27","publication":"The Journal of Chemical Physics","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"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."},{"publisher":"Institute of Science and Technology Austria","oa":1,"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.","page":"215","date_published":"2020-09-08T00:00:00Z","doi":"10.15479/AT:ISTA:8341","date_created":"2020-09-08T08:53:53Z","has_accepted_license":"1","year":"2020","day":"08","author":[{"last_name":"Bezeljak","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"In vitro reconstitution of a Rab activation switch","citation":{"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.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi: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","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"09","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"7580","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"creator":"dernst","date_updated":"2021-09-16T12:49:12Z","file_size":65246782,"date_created":"2020-09-08T09:00:29Z","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"70871b335a595252a66c6bbf0824fb02","file_id":"8342"},{"creator":"dernst","date_updated":"2021-09-16T12:49:12Z","file_size":31259058,"date_created":"2020-09-08T09:00:27Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8343","checksum":"59a62275088b00b7241e6ff4136434c7"}],"language":[{"iso":"eng"}],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","_id":"8341","department":[{"_id":"MaLo"}],"file_date_updated":"2021-09-16T12:49:12Z","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"date_updated":"2023-09-07T13:17:06Z","ddc":["570"]},{"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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"scopus_import":"1","intvolume":" 117","month":"03","publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"volume":117,"issue":"12","related_material":{"record":[{"id":"8341","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release","description":"News on IST Homepage"}]},"_id":"7580","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-07T13:17:06Z","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","year":"2020","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"24","page":"6504-6549","date_created":"2020-03-12T05:32:26Z","date_published":"2020-03-24T00:00:00Z","doi":"10.1073/pnas.1921027117","project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"citation":{"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","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","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000521821800040"]},"article_processing_charge":"No","author":[{"id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban","orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","last_name":"Bezeljak"},{"first_name":"Hrushikesh","full_name":"Loya, Hrushikesh","last_name":"Loya"},{"first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek","full_name":"Kaczmarek, Beata M"},{"last_name":"Saunders","full_name":"Saunders, Timothy E.","first_name":"Timothy E."},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"title":"Stochastic activation and bistability in a Rab GTPase regulatory network"},{"publisher":"Institute of Science and Technology Austria","oa":1,"page":"xviii+120","doi":"10.15479/AT:ISTA:8032","date_published":"2020-06-26T00:00:00Z","date_created":"2020-06-26T10:00:36Z","has_accepted_license":"1","year":"2020","day":"26","author":[{"last_name":"Huszár","full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf"}],"article_processing_charge":"No","title":"Combinatorial width parameters for 3-dimensional manifolds","citation":{"mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","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","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.","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"06","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6556"},{"relation":"dissertation_contains","id":"7093","status":"public"}]},"publication_identifier":{"isbn":["978-3-99078-006-0"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_updated":"2020-07-14T12:48:08Z","file_size":2637562,"creator":"khuszar","date_created":"2020-06-26T10:03:58Z","file_name":"Kristof_Huszar-Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8034","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3"},{"file_id":"8035","checksum":"d5f8456202b32f4a77552ef47a2837d1","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"Kristof_Huszar-Thesis-source.zip","date_created":"2020-06-26T10:10:06Z","creator":"khuszar","file_size":7163491,"date_updated":"2020-07-14T12:48:08Z"}],"language":[{"iso":"eng"}],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"8032","file_date_updated":"2020-07-14T12:48:08Z","department":[{"_id":"UlWa"}],"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"date_updated":"2023-09-07T13:18:27Z","ddc":["514"]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","month":"07","intvolume":" 12224","publication_identifier":{"eisbn":["9783030532888"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030532871"]},"publication_status":"published","file":[{"date_updated":"2020-08-06T08:14:54Z","file_size":804237,"creator":"dernst","date_created":"2020-08-06T08:14:54Z","file_name":"2020_LNCS_Kragl.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8201","success":1}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"volume":12224,"_id":"8195","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"file_date_updated":"2020-08-06T08:14:54Z","department":[{"_id":"ToHe"}],"acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"14","publication":"Computer Aided Verification","page":"275-298","doi":"10.1007/978-3-030-53288-8_14","date_published":"2020-07-14T00:00:00Z","date_created":"2020-08-03T11:45:35Z","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"citation":{"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.","ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","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.","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","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","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in Computer Aided Verification, 2020, vol. 12224, pp. 275–298.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"article_processing_charge":"No","external_id":{"isi":["000695276000014"]},"title":"Refinement for structured concurrent programs"},{"isi":1,"year":"2020","day":"01","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","page":"227-242","date_published":"2020-06-01T00:00:00Z","doi":"10.1145/3385412.3385980","date_created":"2020-06-25T11:40:16Z","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"first_name":"Constantin","full_name":"Enea, Constantin","last_name":"Enea"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Mutluergil","full_name":"Mutluergil, Suha Orhun","first_name":"Suha Orhun"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"external_id":{"isi":["000614622300016"]},"article_processing_charge":"No","title":"Inductive sequentialization of asynchronous programs","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["9781450376136"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"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."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}],"month":"06","date_updated":"2023-09-07T13:18:00Z","department":[{"_id":"ToHe"}],"_id":"8012","type":"conference","conference":{"name":"PLDI: Programming Language Design and Implementation","start_date":"2020-06-15","end_date":"2020-06-20","location":"London, United Kingdom"},"status":"public"},{"supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"}],"date_updated":"2023-09-07T13:18:51Z","ddc":["572"],"department":[{"_id":"MaLo"}],"file_date_updated":"2020-09-11T07:48:10Z","_id":"8358","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-009-1"]},"degree_awarded":"PhD","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8364","checksum":"882f93fe9c351962120e2669b84bf088","success":1,"date_updated":"2020-09-10T12:11:29Z","file_size":141602462,"creator":"pcaldas","date_created":"2020-09-10T12:11:29Z","file_name":"phd_thesis_pcaldas.pdf"},{"file_id":"8365","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"phd_thesis_latex_pcaldas.zip","date_created":"2020-09-10T12:18:17Z","creator":"pcaldas","file_size":450437458,"date_updated":"2020-09-11T07:48:10Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7572","status":"public","relation":"dissertation_contains"},{"status":"public","id":"7197","relation":"part_of_dissertation"}]},"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"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","citation":{"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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R"}],"article_processing_charge":"No","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","has_accepted_license":"1","year":"2020","day":"10","page":"135","doi":"10.15479/AT:ISTA:8358","date_published":"2020-09-10T00:00:00Z","date_created":"2020-09-10T09:26:49Z","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","oa":1},{"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"conference":{"name":"ESA: Annual European Symposium on Algorithms","end_date":"2020-09-09","location":"Virtual, Online; Pisa, Italy","start_date":"2020-09-07"},"type":"conference","status":"public","_id":"8703","department":[{"_id":"HeEd"}],"file_date_updated":"2020-10-27T14:31:52Z","date_updated":"2023-09-07T13:29:00Z","ddc":["000"],"scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 173","month":"08","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/3.0/","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"9056","status":"public"}]},"volume":173,"publication_status":"published","publication_identifier":{"issn":["18688969"],"isbn":["9783959771627"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_LIPIcs_Osang.pdf","date_created":"2020-10-27T14:31:52Z","creator":"cziletti","file_size":733291,"date_updated":"2020-10-27T14:31:52Z","success":1,"file_id":"8712","checksum":"fe0f7c49a99ed870c671b911e10d5496","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"}],"article_number":"75","article_processing_charge":"No","author":[{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116"},{"full_name":"Rouxel-Labbé, Mael","last_name":"Rouxel-Labbé","first_name":"Mael"},{"first_name":"Monique","last_name":"Teillaud","full_name":"Teillaud, Monique"}],"title":"Generalizing CGAL periodic Delaunay triangulations","citation":{"short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_created":"2020-10-25T23:01:18Z","doi":"10.4230/LIPIcs.ESA.2020.75","date_published":"2020-08-26T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"28th Annual European Symposium on Algorithms","day":"26"},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","oa":1,"quality_controlled":"1","month":"04","year":"2020","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"8th International Conference on Learning Representations","file":[{"creator":"bphuong","date_updated":"2020-07-14T12:47:59Z","file_size":405469,"date_created":"2020-02-11T09:07:27Z","file_name":"main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7482","checksum":"8d372ea5defd8cb8fdc430111ed754a9"}],"day":"26","date_created":"2020-02-11T09:07:37Z","related_material":{"link":[{"url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html","relation":"supplementary_material"}],"record":[{"status":"public","id":"9418","relation":"dissertation_contains"}]},"date_published":"2020-04-26T00:00:00Z","_id":"7481","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Online","end_date":"2020-04-30","start_date":"2020-04-27"},"type":"conference","status":"public","citation":{"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.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020.","apa":"Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020."},"date_updated":"2023-09-07T13:29:50Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"ChLa"}],"title":"Functional vs. parametric equivalence of ReLU networks"},{"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"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.08647"}],"scopus_import":"1","intvolume":" 52","month":"02","publication_status":"published","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"}]},"issue":"1","volume":52,"_id":"9781","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"status":"public","date_updated":"2023-09-07T13:30:11Z","ddc":["510"],"department":[{"_id":"RoSe"}],"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.","oa":1,"quality_controlled":"1","publisher":"Society for Industrial & Applied Mathematics ","year":"2020","has_accepted_license":"1","isi":1,"publication":"SIAM Journal on Mathematical Analysis","day":"12","page":"605-622","date_created":"2021-08-06T07:34:16Z","doi":"10.1137/19m126284x","date_published":"2020-02-12T00:00:00Z","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"citation":{"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.","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.","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.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"article_processing_charge":"No","author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball"},{"citation":{"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.","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.","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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"},{"orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"external_id":{"isi":["000511060200001"]},"article_processing_charge":"Yes (via OA deal)","title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"has_accepted_license":"1","year":"2020","day":"01","publication":"Archive for Rational Mechanics and Analysis","page":"967-1087","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/s00205-019-01486-2","date_created":"2020-02-16T23:00:50Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_updated":"2023-09-07T13:30:45Z","ddc":["530","532"],"file_date_updated":"2020-11-20T09:14:22Z","department":[{"_id":"JuFi"}],"_id":"7489","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["00039527"],"eissn":["14320673"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f107e21b58f5930876f47144be37cf6c","file_id":"8779","success":1,"date_updated":"2020-11-20T09:14:22Z","file_size":1897571,"creator":"dernst","date_created":"2020-11-20T09:14:22Z","file_name":"2020_ArchRatMechAn_Fischer.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"10007","status":"public"}]},"volume":236,"ec_funded":1,"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 236"},{"external_id":{"arxiv":["2003.05478"]},"article_processing_charge":"No","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"last_name":"Hensel","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laux","full_name":"Laux, Tim","first_name":"Tim"},{"last_name":"Simon","full_name":"Simon, Thilo","first_name":"Thilo"}],"department":[{"_id":"JuFi"}],"title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","date_updated":"2023-09-07T13:30:45Z","citation":{"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.","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.","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. .","short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).","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.","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"status":"public","_id":"10012","article_number":"2003.05478","date_created":"2021-09-13T12:17:11Z","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10007"}]},"date_published":"2020-03-11T00:00:00Z","year":"2020","publication_status":"submitted","language":[{"iso":"eng"}],"publication":"arXiv","day":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.05478"}],"month":"03","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"}],"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.","oa_version":"Preprint"},{"scopus_import":"1","intvolume":" 14","month":"10","acknowledged_ssus":[{"_id":"NanoFab"}],"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. "}],"oa_version":"Published Version","ec_funded":1,"issue":"4","volume":14,"related_material":{"record":[{"relation":"research_data","id":"13070","status":"public"},{"relation":"dissertation_contains","id":"9920","status":"public"}]},"publication_status":"published","publication_identifier":{"eissn":["23317019"]},"language":[{"iso":"eng"}],"file":[{"file_size":2607823,"date_updated":"2021-03-29T11:43:20Z","creator":"dernst","file_name":"2020_PhysReviewApplied_Peruzzo.pdf","date_created":"2021-03-29T11:43:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"2a634abe75251ae7628cd54c8a4ce2e8","file_id":"9300"}],"type":"journal_article","article_type":"original","status":"public","_id":"8755","department":[{"_id":"JoFi"}],"file_date_updated":"2021-03-29T11:43:20Z","date_updated":"2023-09-07T13:31:22Z","ddc":["530"],"oa":1,"quality_controlled":"1","publisher":"American Physical Society","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). ","date_created":"2020-11-15T23:01:17Z","date_published":"2020-10-29T00:00:00Z","doi":"10.1103/PhysRevApplied.14.044055","year":"2020","isi":1,"has_accepted_license":"1","publication":"Physical Review Applied","day":"29","project":[{"grant_number":"F07105","name":"Integrating superconducting quantum circuits","call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"_id":"257EB838-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"name":"Quantum readout techniques and technologies","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"044055","external_id":{"arxiv":["2007.01644"],"isi":["000582797300003"]},"article_processing_charge":"No","author":[{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","last_name":"Peruzzo"},{"full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"}],"title":"Surpassing the resistance quantum with a geometric superinductor","citation":{"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.","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","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.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Di erential Systems","grant_number":" F06504","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"article_processing_charge":"No","external_id":{"arxiv":["1905.05757"],"isi":["000539439400008"]},"author":[{"last_name":"Gladbach","full_name":"Gladbach, Peter","first_name":"Peter"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"},{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"title":"Homogenisation of one-dimensional discrete optimal transport","citation":{"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.","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","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","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.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Elsevier","quality_controlled":"1","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.","page":"204-234","date_created":"2020-03-08T23:00:47Z","doi":"10.1016/j.matpur.2020.02.008","date_published":"2020-07-01T00:00:00Z","year":"2020","isi":1,"publication":"Journal de Mathematiques Pures et Appliquees","day":"01","type":"journal_article","article_type":"original","status":"public","_id":"7573","department":[{"_id":"JaMa"}],"date_updated":"2023-09-07T13:31:05Z","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"scopus_import":"1","intvolume":" 139","month":"07","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."}],"oa_version":"Preprint","ec_funded":1,"volume":139,"issue":"7","related_material":{"record":[{"relation":"dissertation_contains","id":"10030","status":"public"}]},"publication_status":"published","publication_identifier":{"issn":["00217824"]},"language":[{"iso":"eng"}]},{"article_number":"2008.10962","_id":"10022","status":"public","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"type":"preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","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.","mla":"Forkert, Dominik L., et al. “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. .","short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","ama":"Forkert DL, Maas J, Portinale L. 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."},"date_updated":"2023-09-07T13:31:05Z","department":[{"_id":"JaMa"}],"title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","external_id":{"arxiv":["2008.10962"]},"article_processing_charge":"No","author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","full_name":"Forkert, Dominik L","last_name":"Forkert"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"},{"last_name":"Portinale","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"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.","oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"08","main_file_link":[{"url":"https://arxiv.org/abs/2008.10962","open_access":"1"}],"oa":1,"publication":"arXiv","language":[{"iso":"eng"}],"day":"25","year":"2020","publication_status":"submitted","date_created":"2021-09-17T10:57:27Z","ec_funded":1,"date_published":"2020-08-25T00:00:00Z","related_material":{"record":[{"status":"public","id":"11739","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"10030"}]},"page":"33"},{"publication":"Proceedings of the 37th International Conference on Machine Learning","day":"12","year":"2020","has_accepted_license":"1","date_created":"2020-11-05T15:25:58Z","date_published":"2020-07-12T00:00:00Z","page":"5416-5425","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).","oa":1,"publisher":"ML Research Press","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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.","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.","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."},"title":"On the sample complexity of adversarial multi-source PAC learning","article_processing_charge":"No","external_id":{"arxiv":["2002.10384"]},"author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","first_name":"Elias","full_name":"Frantar, Elias","last_name":"Frantar"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9120","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","success":1,"creator":"dernst","date_updated":"2021-02-15T09:00:01Z","file_size":281286,"date_created":"2021-02-15T09:00:01Z","file_name":"2020_PMLR_Konstantinov.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2640-3498"]},"ec_funded":1,"volume":119,"related_material":{"record":[{"relation":"dissertation_contains","id":"10799","status":"public"}],"link":[{"relation":"supplementary_material","url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 119","month":"07","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-07T13:42:08Z","file_date_updated":"2021-02-15T09:00:01Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"_id":"8724","status":"public","conference":{"name":"ICML: International Conference on Machine Learning","location":"Online","end_date":"2020-07-18","start_date":"2020-07-12"},"type":"conference"},{"related_material":{"record":[{"id":"10759","status":"public","relation":"dissertation_contains"}]},"volume":22,"issue":"9","ec_funded":1,"file":[{"creator":"dernst","file_size":2725143,"date_updated":"2020-10-12T12:18:47Z","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","date_created":"2020-10-12T12:18:47Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8650","checksum":"c9238fff422e7a957c3a0d559f756b3a"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["13672630"]},"publication_status":"published","month":"09","intvolume":" 22","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"file_date_updated":"2020-10-12T12:18:47Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2023-09-07T13:44:16Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8644","doi":"10.1088/1367-2630/abae44","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-11T22:01:14Z","day":"01","publication":"New Journal of Physics","isi":1,"has_accepted_license":"1","year":"2020","quality_controlled":"1","publisher":"IOP Publishing","oa":1,"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).","title":"Detecting composite orders in layered models via machine learning","author":[{"last_name":"Rzadkowski","orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech","first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N","full_name":"Defenu, N","last_name":"Defenu"},{"last_name":"Chiacchiera","full_name":"Chiacchiera, S","first_name":"S"},{"first_name":"A","last_name":"Trombettoni","full_name":"Trombettoni, A"},{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000573298000001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","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.","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.","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.","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."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"25681","name":"Analytic and machine learning approaches to composite quantum impurities","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","name":"A path-integral approach to composite impurities","grant_number":"M02641"}],"article_number":"093026"},{"ec_funded":1,"issue":"12","volume":21,"related_material":{"record":[{"id":"11473","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8711","checksum":"c12c9c1e6f08def245e42f3cb1d83827","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_Annales_Mysliwy.pdf","date_created":"2020-10-27T12:49:04Z","creator":"cziletti","file_size":469831,"date_updated":"2020-10-27T12:49:04Z"}],"scopus_import":"1","intvolume":" 21","month":"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"}],"oa_version":"Published Version","file_date_updated":"2020-10-27T12:49:04Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-07T13:43:51Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"8705","page":"4003-4025","date_created":"2020-10-25T23:01:19Z","date_published":"2020-12-01T00:00:00Z","doi":"10.1007/s00023-020-00969-3","year":"2020","isi":1,"has_accepted_license":"1","publication":"Annales Henri Poincare","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","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)","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2003.12371"],"isi":["000578111800002"]},"author":[{"full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy","first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","citation":{"short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Oxford University Press","quality_controlled":"1","oa":1,"year":"2020","day":"01","publication":"Bioinformatics","page":"i919-i927","date_published":"2020-12-01T00:00:00Z","doi":"10.1093/bioinformatics/btaa843","date_created":"2023-08-21T12:28:20Z","citation":{"mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Stark, Stefan G","last_name":"Stark","first_name":"Stefan G"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"full_name":"Aebersold, Rudolf","last_name":"Aebersold","first_name":"Rudolf"},{"full_name":"Al-Quaddoomi, Faisal S","last_name":"Al-Quaddoomi","first_name":"Faisal S"},{"full_name":"Albinus, Jonas","last_name":"Albinus","first_name":"Jonas"},{"last_name":"Alborelli","full_name":"Alborelli, Ilaria","first_name":"Ilaria"},{"last_name":"Andani","full_name":"Andani, Sonali","first_name":"Sonali"},{"full_name":"Attinger, Per-Olof","last_name":"Attinger","first_name":"Per-Olof"},{"last_name":"Bacac","full_name":"Bacac, Marina","first_name":"Marina"},{"last_name":"Baumhoer","full_name":"Baumhoer, Daniel","first_name":"Daniel"},{"first_name":"Beatrice","full_name":"Beck-Schimmer, Beatrice","last_name":"Beck-Schimmer"},{"full_name":"Beerenwinkel, Niko","last_name":"Beerenwinkel","first_name":"Niko"},{"last_name":"Beisel","full_name":"Beisel, Christian","first_name":"Christian"},{"full_name":"Bernasconi, Lara","last_name":"Bernasconi","first_name":"Lara"},{"first_name":"Anne","last_name":"Bertolini","full_name":"Bertolini, Anne"},{"first_name":"Bernd","full_name":"Bodenmiller, Bernd","last_name":"Bodenmiller"},{"first_name":"Ximena","full_name":"Bonilla, Ximena","last_name":"Bonilla"},{"last_name":"Casanova","full_name":"Casanova, Ruben","first_name":"Ruben"},{"last_name":"Chevrier","full_name":"Chevrier, Stéphane","first_name":"Stéphane"},{"last_name":"Chicherova","full_name":"Chicherova, Natalia","first_name":"Natalia"},{"first_name":"Maya","full_name":"D'Costa, Maya","last_name":"D'Costa"},{"first_name":"Esther","last_name":"Danenberg","full_name":"Danenberg, Esther"},{"first_name":"Natalie","full_name":"Davidson, Natalie","last_name":"Davidson"},{"last_name":"gan","full_name":"gan, Monica-Andreea Dră","first_name":"Monica-Andreea Dră"},{"last_name":"Dummer","full_name":"Dummer, Reinhard","first_name":"Reinhard"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"first_name":"Martin","last_name":"Erkens","full_name":"Erkens, Martin"},{"full_name":"Eschbach, Katja","last_name":"Eschbach","first_name":"Katja"},{"first_name":"Cinzia","last_name":"Esposito","full_name":"Esposito, Cinzia"},{"full_name":"Fedier, André","last_name":"Fedier","first_name":"André"},{"first_name":"Pedro","last_name":"Ferreira","full_name":"Ferreira, Pedro"},{"last_name":"Ficek","full_name":"Ficek, Joanna","first_name":"Joanna"},{"last_name":"Frei","full_name":"Frei, Anja L","first_name":"Anja L"},{"full_name":"Frey, Bruno","last_name":"Frey","first_name":"Bruno"},{"last_name":"Goetze","full_name":"Goetze, Sandra","first_name":"Sandra"},{"last_name":"Grob","full_name":"Grob, Linda","first_name":"Linda"},{"first_name":"Gabriele","last_name":"Gut","full_name":"Gut, Gabriele"},{"first_name":"Detlef","full_name":"Günther, Detlef","last_name":"Günther"},{"first_name":"Martina","last_name":"Haberecker","full_name":"Haberecker, Martina"},{"last_name":"Haeuptle","full_name":"Haeuptle, Pirmin","first_name":"Pirmin"},{"last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola","first_name":"Viola"},{"last_name":"Herter","full_name":"Herter, Sylvia","first_name":"Sylvia"},{"full_name":"Holtackers, Rene","last_name":"Holtackers","first_name":"Rene"},{"full_name":"Huesser, Tamara","last_name":"Huesser","first_name":"Tamara"},{"first_name":"Anja","last_name":"Irmisch","full_name":"Irmisch, Anja"},{"full_name":"Jacob, Francis","last_name":"Jacob","first_name":"Francis"},{"last_name":"Jacobs","full_name":"Jacobs, Andrea","first_name":"Andrea"},{"first_name":"Tim M","last_name":"Jaeger","full_name":"Jaeger, Tim M"},{"first_name":"Katharina","full_name":"Jahn, Katharina","last_name":"Jahn"},{"full_name":"James, Alva R","last_name":"James","first_name":"Alva R"},{"first_name":"Philip M","last_name":"Jermann","full_name":"Jermann, Philip M"},{"full_name":"Kahles, André","last_name":"Kahles","first_name":"André"},{"first_name":"Abdullah","last_name":"Kahraman","full_name":"Kahraman, Abdullah"},{"first_name":"Viktor H","last_name":"Koelzer","full_name":"Koelzer, Viktor H"},{"full_name":"Kuebler, Werner","last_name":"Kuebler","first_name":"Werner"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"first_name":"Christian P","full_name":"Kunze, Christian P","last_name":"Kunze"},{"full_name":"Kurzeder, Christian","last_name":"Kurzeder","first_name":"Christian"},{"first_name":"Kjong-Van","last_name":"Lehmann","full_name":"Lehmann, Kjong-Van"},{"first_name":"Mitchell","full_name":"Levesque, Mitchell","last_name":"Levesque"},{"first_name":"Sebastian","last_name":"Lugert","full_name":"Lugert, Sebastian"},{"last_name":"Maass","full_name":"Maass, Gerd","first_name":"Gerd"},{"full_name":"Manz, Markus","last_name":"Manz","first_name":"Markus"},{"first_name":"Philipp","full_name":"Markolin, Philipp","last_name":"Markolin"},{"last_name":"Mena","full_name":"Mena, Julien","first_name":"Julien"},{"first_name":"Ulrike","full_name":"Menzel, Ulrike","last_name":"Menzel"},{"first_name":"Julian M","full_name":"Metzler, Julian M","last_name":"Metzler"},{"last_name":"Miglino","full_name":"Miglino, Nicola","first_name":"Nicola"},{"first_name":"Emanuela S","full_name":"Milani, Emanuela S","last_name":"Milani"},{"last_name":"Moch","full_name":"Moch, Holger","first_name":"Holger"},{"first_name":"Simone","full_name":"Muenst, Simone","last_name":"Muenst"},{"first_name":"Riccardo","last_name":"Murri","full_name":"Murri, Riccardo"},{"full_name":"Ng, Charlotte KY","last_name":"Ng","first_name":"Charlotte KY"},{"first_name":"Stefan","last_name":"Nicolet","full_name":"Nicolet, Stefan"},{"full_name":"Nowak, Marta","last_name":"Nowak","first_name":"Marta"},{"first_name":"Patrick GA","last_name":"Pedrioli","full_name":"Pedrioli, Patrick GA"},{"last_name":"Pelkmans","full_name":"Pelkmans, Lucas","first_name":"Lucas"},{"first_name":"Salvatore","last_name":"Piscuoglio","full_name":"Piscuoglio, Salvatore"},{"first_name":"Michael","last_name":"Prummer","full_name":"Prummer, Michael"},{"first_name":"Mathilde","full_name":"Ritter, Mathilde","last_name":"Ritter"},{"full_name":"Rommel, Christian","last_name":"Rommel","first_name":"Christian"},{"first_name":"María L","full_name":"Rosano-González, María L","last_name":"Rosano-González"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Natascha","last_name":"Santacroce","full_name":"Santacroce, Natascha"},{"first_name":"Jacobo Sarabia del","last_name":"Castillo","full_name":"Castillo, Jacobo Sarabia del"},{"first_name":"Ramona","last_name":"Schlenker","full_name":"Schlenker, Ramona"},{"full_name":"Schwalie, Petra C","last_name":"Schwalie","first_name":"Petra C"},{"full_name":"Schwan, Severin","last_name":"Schwan","first_name":"Severin"},{"first_name":"Tobias","full_name":"Schär, Tobias","last_name":"Schär"},{"first_name":"Gabriela","full_name":"Senti, Gabriela","last_name":"Senti"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"first_name":"Sujana","full_name":"Sivapatham, Sujana","last_name":"Sivapatham"},{"full_name":"Snijder, Berend","last_name":"Snijder","first_name":"Berend"},{"first_name":"Bettina","full_name":"Sobottka, Bettina","last_name":"Sobottka"},{"last_name":"Sreedharan","full_name":"Sreedharan, Vipin T","first_name":"Vipin T"},{"first_name":"Stefan","full_name":"Stark, Stefan","last_name":"Stark"},{"first_name":"Daniel J","last_name":"Stekhoven","full_name":"Stekhoven, Daniel J"},{"last_name":"Theocharides","full_name":"Theocharides, Alexandre PA","first_name":"Alexandre PA"},{"last_name":"Thomas","full_name":"Thomas, Tinu M","first_name":"Tinu M"},{"first_name":"Markus","full_name":"Tolnay, Markus","last_name":"Tolnay"},{"first_name":"Vinko","last_name":"Tosevski","full_name":"Tosevski, Vinko"},{"full_name":"Toussaint, Nora C","last_name":"Toussaint","first_name":"Nora C"},{"full_name":"Tuncel, Mustafa A","last_name":"Tuncel","first_name":"Mustafa A"},{"full_name":"Tusup, Marina","last_name":"Tusup","first_name":"Marina"},{"first_name":"Audrey Van","last_name":"Drogen","full_name":"Drogen, Audrey Van"},{"first_name":"Marcus","full_name":"Vetter, Marcus","last_name":"Vetter"},{"last_name":"Vlajnic","full_name":"Vlajnic, Tatjana","first_name":"Tatjana"},{"last_name":"Weber","full_name":"Weber, Sandra","first_name":"Sandra"},{"last_name":"Weber","full_name":"Weber, Walter P","first_name":"Walter P"},{"first_name":"Rebekka","last_name":"Wegmann","full_name":"Wegmann, Rebekka"},{"first_name":"Michael","last_name":"Weller","full_name":"Weller, Michael"},{"last_name":"Wendt","full_name":"Wendt, Fabian","first_name":"Fabian"},{"full_name":"Wey, Norbert","last_name":"Wey","first_name":"Norbert"},{"last_name":"Wicki","full_name":"Wicki, Andreas","first_name":"Andreas"},{"first_name":"Bernd","full_name":"Wollscheid, Bernd","last_name":"Wollscheid"},{"first_name":"Shuqing","last_name":"Yu","full_name":"Yu, Shuqing"},{"first_name":"Johanna","last_name":"Ziegler","full_name":"Ziegler, Johanna"},{"first_name":"Marc","full_name":"Zimmermann, Marc","last_name":"Zimmermann"},{"first_name":"Martin","last_name":"Zoche","full_name":"Zoche, Martin"},{"last_name":"Zuend","full_name":"Zuend, Gregor","first_name":"Gregor"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"last_name":"Lehmann","full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van"}],"article_processing_charge":"No","external_id":{"pmid":["33381818"]},"title":"SCIM: Universal single-cell matching with unpaired feature sets","abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"month":"12","intvolume":" 36","publication_identifier":{"eissn":["1367-4811"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"Supplement_2","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"volume":36,"_id":"14125","article_type":"original","type":"journal_article","status":"public","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"date_updated":"2023-09-11T10:21:00Z","extern":"1","department":[{"_id":"FrLo"}]},{"department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T07:44:48Z","extern":"1","conference":{"end_date":"2020-02-12","location":"New York, NY, United States","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"type":"conference","status":"public","_id":"14186","issue":"9","volume":34,"publication_status":"published","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781577358350"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14184"}],"scopus_import":"1","intvolume":" 34","month":"07","abstract":[{"text":"The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research.","lang":"eng"}],"oa_version":"Preprint","external_id":{"arxiv":["2007.14184"]},"article_processing_charge":"No","author":[{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"title":"A commentary on the unsupervised learning of disentangled representations","citation":{"ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120.","ieee":"F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"13681-13684","date_created":"2023-08-22T14:07:26Z","date_published":"2020-07-28T00:00:00Z","doi":"10.1609/aaai.v34i09.7120","year":"2020","publication":"The 34th AAAI Conference on Artificial Intelligence","day":"28","oa":1,"publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359.","chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.","apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359.","short":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359.","mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359."},"title":"Weakly-supervised disentanglement without compromises","author":[{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Ben","full_name":"Poole, Ben","last_name":"Poole"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"}],"external_id":{"arxiv":["2002.02886"]},"article_processing_charge":"No","quality_controlled":"1","oa":1,"day":"07","publication":"Proceedings of the 37th International Conference on Machine Learning","year":"2020","date_published":"2020-07-07T00:00:00Z","date_created":"2023-08-22T14:08:14Z","page":"6348–6359","_id":"14188","status":"public","type":"conference","conference":{"name":"International Conference on Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13"},"extern":"1","date_updated":"2023-09-12T07:59:29Z","department":[{"_id":"FrLo"}],"oa_version":"Preprint","abstract":[{"text":"Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios.","lang":"eng"}],"month":"07","intvolume":" 119","scopus_import":"1","alternative_title":["PMLR"],"main_file_link":[{"url":"https://arxiv.org/abs/2002.02886","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":119},{"_id":"14187","type":"conference","conference":{"name":"International Conference on Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13"},"status":"public","date_updated":"2023-09-12T08:03:40Z","citation":{"mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.","apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual.","ieee":"G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262.","short":"G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262.","chicago":"Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020.","ista":"Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Geoffrey","last_name":"Négiar","full_name":"Négiar, Geoffrey"},{"full_name":"Dresdner, Gideon","last_name":"Dresdner","first_name":"Gideon"},{"first_name":"Alicia","last_name":"Tsai","full_name":"Tsai, Alicia"},{"first_name":"Laurent El","last_name":"Ghaoui","full_name":"Ghaoui, Laurent El"},{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"full_name":"Freund, Robert M.","last_name":"Freund","first_name":"Robert M."},{"last_name":"Pedregosa","full_name":"Pedregosa, Fabian","first_name":"Fabian"}],"article_processing_charge":"No","external_id":{"arxiv":["2002.11860"]},"department":[{"_id":"FrLo"}],"title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","abstract":[{"lang":"eng","text":"We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package."}],"oa_version":"Preprint","quality_controlled":"1","alternative_title":["PMLR"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.11860"}],"oa":1,"month":"07","intvolume":" 119","year":"2020","publication_status":"published","day":"27","publication":"Proceedings of the 37th International Conference on Machine Learning","language":[{"iso":"eng"}],"page":"7253-7262","date_published":"2020-07-27T00:00:00Z","volume":119,"date_created":"2023-08-22T14:07:52Z"},{"title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","article_processing_charge":"No","external_id":{"arxiv":["2010.14766"]},"author":[{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. MIT Press.","ama":"Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 2020;21.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020).","ieee":"F. Locatello et al., “A sober look at the unsupervised learning of disentangled representations and their evaluation,” Journal of Machine Learning Research, vol. 21. MIT Press, 2020.","mla":"Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research. MIT Press, 2020."},"article_number":"209","date_created":"2023-08-22T14:10:34Z","date_published":"2020-09-01T00:00:00Z","publication":"Journal of Machine Learning Research","day":"01","year":"2020","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"MIT Press","department":[{"_id":"FrLo"}],"ddc":["000"],"extern":"1","date_updated":"2023-09-12T09:23:56Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14195","volume":21,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 21","month":"09","main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets.","lang":"eng"}]},{"citation":{"short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","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.","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","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","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.","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000526725200019"]},"article_processing_charge":"No","author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"title":"The relation between crosstalk and gene regulation form revisited","article_number":"e1007642","year":"2020","isi":1,"has_accepted_license":"1","publication":"PLOS Computational Biology","day":"25","date_created":"2020-03-06T07:39:38Z","doi":"10.1371/journal.pcbi.1007642","date_published":"2020-02-25T00:00:00Z","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","date_updated":"2023-09-12T11:02:24Z","ddc":["000","570"],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:00Z","_id":"7569","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["1553-7358"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_PlosCompBio_Grah.pdf","date_created":"2020-03-09T15:12:21Z","creator":"dernst","file_size":2209325,"date_updated":"2020-07-14T12:48:00Z","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","file_id":"7579","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"issue":"2","volume":16,"related_material":{"record":[{"relation":"research_data","id":"9716","status":"deleted"},{"id":"9776","status":"public","relation":"research_data"},{"relation":"used_in_publication","id":"9779","status":"public"},{"id":"8155","status":"public","relation":"dissertation_contains"},{"status":"public","id":"9777","relation":"research_data"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 16","month":"02"},{"_id":"8813","status":"public","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.).","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","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","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","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."},"date_updated":"2023-09-12T11:05:28Z","department":[{"_id":"SiHi"}],"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","author":[{"last_name":"Santini","full_name":"Santini, Laura","first_name":"Laura"},{"last_name":"Halbritter","full_name":"Halbritter, Florian","first_name":"Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"first_name":"Toru","full_name":"Suzuki, Toru","last_name":"Suzuki"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"last_name":"Lackner","full_name":"Lackner, Andreas","first_name":"Andreas"},{"full_name":"Warr, Nick","last_name":"Warr","first_name":"Nick"},{"last_name":"Pauler","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"full_name":"Laue, Ernest","last_name":"Laue","first_name":"Ernest"},{"full_name":"Farlik, Matthias","last_name":"Farlik","first_name":"Matthias"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C. F.","last_name":"Perry","first_name":"Anthony C. F."},{"last_name":"Leeb","full_name":"Leeb, Martin","first_name":"Martin"}],"external_id":{"pmid":["PPR234457 "]},"article_processing_charge":"No","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"11","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.03.366948"}],"oa":1,"day":"05","language":[{"iso":"eng"}],"publication":"bioRxiv","publication_status":"submitted","year":"2020","doi":"10.1101/2020.11.03.366948","date_published":"2020-11-05T00:00:00Z","date_created":"2020-11-26T07:17:19Z"},{"year":"2020","day":"25","doi":"10.1371/journal.pcbi.1007642.s002","related_material":{"record":[{"id":"7569","status":"public","relation":"used_in_publication"}]},"date_published":"2020-02-25T00:00:00Z","date_created":"2021-08-06T07:21:51Z","oa_version":"None","publisher":"Public Library of Science","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pcbi.1007642.s002"}],"oa":1,"month":"02","date_updated":"2023-09-12T11:02:25Z","citation":{"ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, (2020).","apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.","ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"}],"article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Maximizing crosstalk","_id":"9777","type":"research_data_reference","status":"public"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","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.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332"},"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"03","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:8332","date_published":"2020-09-03T00:00:00Z","date_created":"2020-09-04T12:24:12Z","page":"120","_id":"8332","status":"public","type":"dissertation","ddc":["000"],"supervisor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"date_updated":"2023-09-13T08:45:08Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-09-04T13:00:17Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"month":"09","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2020-09-04T12:17:47Z","file_size":1348815,"creator":"bkragl","date_created":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"26fe261550f691280bda4c454bf015c7","file_id":"8333"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","date_updated":"2020-09-04T13:00:17Z","file_size":372312,"creator":"bkragl","date_created":"2020-09-04T13:00:17Z","file_name":"kragl-thesis.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"133","status":"public"},{"id":"8012","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8195","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"160"}]}},{"type":"conference","conference":{"start_date":"2020-12-06","end_date":"2020-12-12","location":"Virtual","name":"NeurIPS: Neural Information Processing Systems"},"status":"public","_id":"14326","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Weissenborn","full_name":"Weissenborn, Dirk","first_name":"Dirk"},{"last_name":"Unterthiner","full_name":"Unterthiner, Thomas","first_name":"Thomas"},{"last_name":"Mahendran","full_name":"Mahendran, Aravindh","first_name":"Aravindh"},{"first_name":"Georg","full_name":"Heigold, Georg","last_name":"Heigold"},{"last_name":"Uszkoreit","full_name":"Uszkoreit, Jakob","first_name":"Jakob"},{"full_name":"Dosovitskiy, Alexey","last_name":"Dosovitskiy","first_name":"Alexey"},{"first_name":"Thomas","full_name":"Kipf, Thomas","last_name":"Kipf"}],"external_id":{"arxiv":["2006.15055"]},"article_processing_charge":"No","department":[{"_id":"FrLo"}],"title":"Object-centric learning with slot attention","citation":{"apa":"Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Curran Associates.","ama":"Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11525-11538.","ieee":"F. Locatello et al., “Object-centric learning with slot attention,” in Advances in Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538.","short":"F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538.","mla":"Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38.","ista":"Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538.","chicago":"Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In Advances in Neural Information Processing Systems, 33:11525–38. Curran Associates, 2020."},"date_updated":"2023-09-13T12:19:19Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Curran Associates","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2006.15055"}],"intvolume":" 33","abstract":[{"lang":"eng","text":"Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n"}],"oa_version":"Preprint","page":"11525-11538","volume":33,"date_published":"2020-01-01T00:00:00Z","date_created":"2023-09-13T12:03:46Z","publication_identifier":{"isbn":["9781713829546"]},"publication_status":"published","year":"2020","language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems"},{"author":[{"full_name":"Gladbach, Peter","last_name":"Gladbach","first_name":"Peter"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"}],"publist_id":"7983","external_id":{"isi":["000546975100017"],"arxiv":["1809.01092"]},"article_processing_charge":"No","title":"Scaling limits of discrete optimal transport","citation":{"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.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802.","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.","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","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","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.","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2759-2802","doi":"10.1137/19M1243440","date_published":"2020-10-01T00:00:00Z","date_created":"2018-12-11T11:44:28Z","isi":1,"year":"2020","day":"01","publication":"SIAM Journal on Mathematical Analysis","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":1,"department":[{"_id":"JaMa"}],"date_updated":"2023-09-18T08:13:15Z","type":"journal_article","article_type":"original","status":"public","_id":"71","issue":"3","volume":52,"publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01092"}],"month":"10","intvolume":" 52","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"}],"oa_version":"Preprint"},{"type":"journal_article","article_type":"original","status":"public","_id":"5681","department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:34:53Z","date_updated":"2023-09-18T09:30:01Z","ddc":["006"],"scopus_import":"1","month":"06","intvolume":" 26","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Submitted Version","issue":"6","volume":26,"publication_identifier":{"eissn":["19410506"],"issn":["10772626"]},"publication_status":"published","file":[{"file_size":21910098,"date_updated":"2020-10-08T08:34:53Z","creator":"wojtan","file_name":"preprint.pdf","date_created":"2020-10-08T08:34:53Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"8d4c55443a0ee335bb5bb652de503042","file_id":"8626"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Hikaru, Ibayashi","last_name":"Hikaru","first_name":"Ibayashi"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"last_name":"Igarashi","full_name":"Igarashi, Takeo","first_name":"Takeo"},{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"}],"article_processing_charge":"No","external_id":{"isi":["000532295600014"],"pmid":["30507534"]},"title":"Simulating liquids on dynamically warping grids","citation":{"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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"IEEE","oa":1,"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.","page":"2288-2302","doi":"10.1109/TVCG.2018.2883628","date_published":"2020-06-01T00:00:00Z","date_created":"2018-12-16T22:59:21Z","has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"IEEE Transactions on Visualization and Computer Graphics"},{"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.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","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.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Xiang"}],"article_processing_charge":"No","title":"Rotation of coupled cold molecules in the presence of a many-body environment","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"has_accepted_license":"1","year":"2020","day":"21","page":"125","date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8958","date_created":"2020-12-21T09:44:30Z","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"date_updated":"2023-09-20T11:30:58Z","ddc":["539"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-12-30T07:18:03Z","_id":"8958","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8967","checksum":"3994c54a1241451d561db1d4f43bad30","file_size":3622305,"date_updated":"2020-12-22T10:55:56Z","creator":"xli","file_name":"THESIS_Xiang_Li.pdf","date_created":"2020-12-22T10:55:56Z"},{"checksum":"0954ecfc5554c05615c14de803341f00","file_id":"8968","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip","date_updated":"2020-12-30T07:18:03Z","file_size":4018859,"creator":"xli"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"5886","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8587"},{"id":"1120","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"12"},{"project":[{"name":"Distributed 3D Object Design","grant_number":"642841","call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","author":[{"orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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."},"publisher":"Institute of Science and Technology Austria","oa":1,"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.","date_published":"2020-09-14T00:00:00Z","doi":"10.15479/AT:ISTA:8386","date_created":"2020-09-14T01:04:53Z","page":"148","day":"14","has_accepted_license":"1","year":"2020","status":"public","type":"dissertation","_id":"8386","department":[{"_id":"BeBi"}],"file_date_updated":"2020-09-15T12:51:53Z","ddc":["003"],"supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"date_updated":"2023-09-22T09:49:31Z","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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"}],"acknowledged_ssus":[{"_id":"SSU"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"486","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1002"}]},"ec_funded":1,"file":[{"date_created":"2020-09-14T01:02:59Z","file_name":"Thesis_Ran.zip","date_updated":"2020-09-14T12:18:43Z","file_size":1245800191,"creator":"rzhang","file_id":"8388","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"},{"creator":"rzhang","date_updated":"2020-09-15T12:51:53Z","file_size":161385316,"date_created":"2020-09-15T12:51:53Z","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"817e20c33be9247f906925517c56a40d","file_id":"8396","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD"},{"citation":{"ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","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.","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Kukucka","full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","has_accepted_license":"1","year":"2020","day":"22","page":"178","date_published":"2020-06-22T00:00:00Z","doi":"10.15479/AT:ISTA:7996","date_created":"2020-06-22T09:22:23Z","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"date_updated":"2023-09-26T15:50:22Z","ddc":["530"],"department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:48:07Z","_id":"7996","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"467e52feb3e361ce8cf5fe8d5c254ece","file_id":"7997","access_level":"closed","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2020-06-22T09:22:04Z","file_name":"JK_thesis_latex_source_files.zip","creator":"dernst","date_updated":"2020-07-14T12:48:07Z","file_size":392794743},{"file_name":"PhD_thesis_JK_pdfa.pdf","date_created":"2020-06-22T09:21:29Z","file_size":28453247,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst","file_id":"7998","checksum":"1de716bf110dbd77d383e479232bf496","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1328","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7541"},{"relation":"part_of_dissertation","id":"77","status":"public"},{"id":"23","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"840","status":"public"}]},"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06"}]