[{"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"25","publication":"PLOS Computational Biology","date_published":"2020-02-25T00:00:00Z","doi":"10.1371/journal.pcbi.1007642","date_created":"2020-03-06T07:39:38Z","article_number":"e1007642","citation":{"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.","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.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","apa":"Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar"}],"article_processing_charge":"No","external_id":{"isi":["000526725200019"]},"title":"The relation between crosstalk and gene regulation form revisited","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","month":"02","intvolume":" 16","publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","file":[{"checksum":"5239dd134dc6e1c71fe7b3ce2953da37","file_id":"7579","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-03-09T15:12:21Z","file_name":"2020_PlosCompBio_Grah.pdf","date_updated":"2020-07-14T12:48:00Z","file_size":2209325,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"2","related_material":{"record":[{"id":"9716","status":"deleted","relation":"research_data"},{"relation":"research_data","id":"9776","status":"public"},{"relation":"used_in_publication","id":"9779","status":"public"},{"status":"public","id":"8155","relation":"dissertation_contains"},{"relation":"research_data","status":"public","id":"9777"}]},"volume":16,"_id":"7569","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)"},"status":"public","date_updated":"2023-09-12T11:02:24Z","ddc":["000","570"],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:00Z"},{"_id":"8813","type":"preprint","status":"public","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.","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","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.).","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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["PPR234457 "]},"author":[{"last_name":"Santini","full_name":"Santini, Laura","first_name":"Laura"},{"last_name":"Halbritter","full_name":"Halbritter, Florian","first_name":"Florian"},{"first_name":"Fabian","full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira"},{"last_name":"Suzuki","full_name":"Suzuki, Toru","first_name":"Toru"},{"first_name":"Maki","full_name":"Asami, Maki","last_name":"Asami"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"last_name":"Ma","full_name":"Ma, Xiaoyan","first_name":"Xiaoyan"},{"first_name":"Andreas","full_name":"Lackner, Andreas","last_name":"Lackner"},{"full_name":"Warr, Nick","last_name":"Warr","first_name":"Nick"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"last_name":"Farlik","full_name":"Farlik, Matthias","first_name":"Matthias"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"last_name":"Beyer","full_name":"Beyer, Andreas","first_name":"Andreas"},{"last_name":"Perry","full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F."},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"}],"department":[{"_id":"SiHi"}],"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","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."}],"pmid":1,"oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","month":"11","publication_status":"submitted","year":"2020","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"05","date_created":"2020-11-26T07:17:19Z","doi":"10.1101/2020.11.03.366948","date_published":"2020-11-05T00:00:00Z"},{"date_created":"2021-08-06T07:21:51Z","related_material":{"record":[{"status":"public","id":"7569","relation":"used_in_publication"}]},"doi":"10.1371/journal.pcbi.1007642.s002","date_published":"2020-02-25T00:00:00Z","year":"2020","day":"25","main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}],"oa":1,"publisher":"Public Library of Science","month":"02","oa_version":"None","article_processing_charge":"No","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar"}],"title":"Maximizing crosstalk","department":[{"_id":"GaTk"}],"citation":{"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.","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002","apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002."},"date_updated":"2023-09-12T11:02:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","status":"public","_id":"9777"},{"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":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"}],"article_processing_charge":"No","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","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["000"],"supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"date_updated":"2023-09-13T08:45:08Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-09-04T13:00:17Z","_id":"8332","status":"public","type":"dissertation","file":[{"file_id":"8333","checksum":"26fe261550f691280bda4c454bf015c7","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf","date_updated":"2020-09-04T12:17:47Z","file_size":1348815,"creator":"bkragl"},{"checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"kragl-thesis.zip","date_created":"2020-09-04T13:00:17Z","file_size":372312,"date_updated":"2020-09-04T13:00:17Z","creator":"bkragl"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"133","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8012"},{"relation":"part_of_dissertation","status":"public","id":"8195"},{"relation":"part_of_dissertation","status":"public","id":"160"}]},"oa_version":"Published Version","abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"]},{"date_updated":"2023-09-13T12:19:19Z","citation":{"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.","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.","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.","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.","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.","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Weissenborn, Dirk","last_name":"Weissenborn","first_name":"Dirk"},{"last_name":"Unterthiner","full_name":"Unterthiner, Thomas","first_name":"Thomas"},{"first_name":"Aravindh","last_name":"Mahendran","full_name":"Mahendran, Aravindh"},{"first_name":"Georg","full_name":"Heigold, Georg","last_name":"Heigold"},{"last_name":"Uszkoreit","full_name":"Uszkoreit, Jakob","first_name":"Jakob"},{"last_name":"Dosovitskiy","full_name":"Dosovitskiy, Alexey","first_name":"Alexey"},{"first_name":"Thomas","full_name":"Kipf, Thomas","last_name":"Kipf"}],"article_processing_charge":"No","external_id":{"arxiv":["2006.15055"]},"department":[{"_id":"FrLo"}],"title":"Object-centric learning with slot attention","_id":"14326","type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2020-12-12","location":"Virtual","start_date":"2020-12-06"},"status":"public","publication_identifier":{"isbn":["9781713829546"]},"year":"2020","publication_status":"published","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"page":"11525-11538","date_published":"2020-01-01T00:00:00Z","volume":33,"date_created":"2023-09-13T12:03:46Z","abstract":[{"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","lang":"eng"}],"oa_version":"Preprint","quality_controlled":"1","publisher":"Curran Associates","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2006.15055"}],"oa":1,"intvolume":" 33"},{"page":"2759-2802","date_created":"2018-12-11T11:44:28Z","doi":"10.1137/19M1243440","date_published":"2020-10-01T00:00:00Z","year":"2020","isi":1,"publication":"SIAM Journal on Mathematical Analysis","day":"01","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","article_processing_charge":"No","external_id":{"arxiv":["1809.01092"],"isi":["000546975100017"]},"author":[{"first_name":"Peter","last_name":"Gladbach","full_name":"Gladbach, Peter"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7983","title":"Scaling limits of discrete optimal transport","citation":{"chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.","mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.","apa":"Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"3","volume":52,"publication_status":"published","publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}],"scopus_import":"1","intvolume":" 52","month":"10","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","department":[{"_id":"JaMa"}],"date_updated":"2023-09-18T08:13:15Z","type":"journal_article","article_type":"original","status":"public","_id":"71"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","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","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.","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."},"title":"Simulating liquids on dynamically warping grids","article_processing_charge":"No","external_id":{"isi":["000532295600014"],"pmid":["30507534"]},"author":[{"first_name":"Ibayashi","full_name":"Hikaru, Ibayashi","last_name":"Hikaru"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"last_name":"Thuerey","full_name":"Thuerey, Nils","first_name":"Nils"},{"last_name":"Igarashi","full_name":"Igarashi, Takeo","first_name":"Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"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.","oa":1,"publisher":"IEEE","quality_controlled":"1","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"01","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2018-12-16T22:59:21Z","date_published":"2020-06-01T00:00:00Z","doi":"10.1109/TVCG.2018.2883628","page":"2288-2302","_id":"5681","status":"public","article_type":"original","type":"journal_article","ddc":["006"],"date_updated":"2023-09-18T09:30:01Z","file_date_updated":"2020-10-08T08:34:53Z","department":[{"_id":"ChWo"}],"oa_version":"Submitted Version","pmid":1,"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."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 26","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8626","checksum":"8d4c55443a0ee335bb5bb652de503042","creator":"wojtan","file_size":21910098,"date_updated":"2020-10-08T08:34:53Z","file_name":"preprint.pdf","date_created":"2020-10-08T08:34:53Z"}],"publication_status":"published","publication_identifier":{"eissn":["19410506"],"issn":["10772626"]},"volume":26,"issue":"6"},{"project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","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."},"title":"Rotation of coupled cold molecules in the presence of a many-body environment","author":[{"last_name":"Li","full_name":"Li, Xiang","first_name":"Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"21","has_accepted_license":"1","year":"2020","date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8958","date_created":"2020-12-21T09:44:30Z","page":"125","_id":"8958","status":"public","type":"dissertation","ddc":["539"],"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","file_date_updated":"2020-12-30T07:18:03Z","department":[{"_id":"MiLe"}],"oa_version":"Published Version","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."}],"month":"12","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2020-12-22T10:55:56Z","file_name":"THESIS_Xiang_Li.pdf","creator":"xli","date_updated":"2020-12-22T10:55:56Z","file_size":3622305,"file_id":"8967","checksum":"3994c54a1241451d561db1d4f43bad30","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_name":"THESIS_Xiang_Li.zip","date_created":"2020-12-22T10:56:03Z","creator":"xli","file_size":4018859,"date_updated":"2020-12-30T07:18:03Z","checksum":"0954ecfc5554c05615c14de803341f00","file_id":"8968","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5886"},{"relation":"part_of_dissertation","id":"8587","status":"public"},{"id":"1120","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1},{"project":[{"name":"Distributed 3D Object Design","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"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.","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"}],"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","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.","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"14","page":"148","date_created":"2020-09-14T01:04:53Z","doi":"10.15479/AT:ISTA:8386","date_published":"2020-09-14T00:00:00Z","_id":"8386","type":"dissertation","status":"public","date_updated":"2023-09-22T09:49:31Z","supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"ddc":["003"],"file_date_updated":"2020-09-15T12:51:53Z","department":[{"_id":"BeBi"}],"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"8388","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","date_updated":"2020-09-14T12:18:43Z","file_size":1245800191,"creator":"rzhang","date_created":"2020-09-14T01:02:59Z","file_name":"Thesis_Ran.zip"},{"success":1,"file_id":"8396","checksum":"817e20c33be9247f906925517c56a40d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","date_created":"2020-09-15T12:51:53Z","file_size":161385316,"date_updated":"2020-09-15T12:51:53Z","creator":"rzhang"}],"ec_funded":1,"related_material":{"record":[{"id":"486","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1002","status":"public"}]}},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","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","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","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.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria."},"title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","article_processing_charge":"No","author":[{"last_name":"Kukucka","full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"}],"day":"22","year":"2020","has_accepted_license":"1","date_created":"2020-06-22T09:22:23Z","date_published":"2020-06-22T00:00:00Z","doi":"10.15479/AT:ISTA:7996","page":"178","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["530"],"date_updated":"2023-09-26T15:50:22Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:48:07Z","_id":"7996","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_size":392794743,"date_updated":"2020-07-14T12:48:07Z","creator":"dernst","file_name":"JK_thesis_latex_source_files.zip","date_created":"2020-06-22T09:22:04Z","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"closed","file_id":"7997","checksum":"467e52feb3e361ce8cf5fe8d5c254ece"},{"creator":"dernst","date_updated":"2020-07-14T12:48:07Z","file_size":28453247,"date_created":"2020-06-22T09:21:29Z","file_name":"PhD_thesis_JK_pdfa.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7998","checksum":"1de716bf110dbd77d383e479232bf496"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"1328","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7541"},{"id":"77","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"23","status":"public"},{"relation":"part_of_dissertation","id":"840","status":"public"}]},"oa_version":"Published Version","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"}],"month":"06","alternative_title":["ISTA Thesis"]}]