[{"abstract":[{"text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:\r\n1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.","lang":"eng"}],"type":"preprint","article_number":"1903.06981","oa_version":"Preprint","date_updated":"2024-01-04T12:42:08Z","date_created":"2020-06-08T12:25:25Z","related_material":{"record":[{"id":"7944","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"later_version","id":"12833"}]},"author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"full_name":"Jain, Kshitij","first_name":"Kshitij","last_name":"Jain"},{"last_name":"Lubiw","first_name":"Anna","full_name":"Lubiw, Anna"},{"first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"},{"full_name":"Miltzow, Tillmann","first_name":"Tillmann","last_name":"Miltzow"},{"last_name":"Mondal","first_name":"Debajyoti","full_name":"Mondal, Debajyoti"},{"first_name":"Anurag Murty","last_name":"Naredla","full_name":"Naredla, Anurag Murty"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"full_name":"Turcotte, Alexi","last_name":"Turcotte","first_name":"Alexi"}],"department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"status":"public","publication_status":"submitted","title":"Token swapping on trees","_id":"7950","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"16","month":"03","language":[{"iso":"eng"}],"date_published":"2019-03-16T00:00:00Z","citation":{"short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d.","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.","ieee":"A. Biniaz et al., “Token swapping on trees,” arXiv. .","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. arXiv.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981."},"external_id":{"arxiv":["1903.06981"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06981"}],"oa":1,"publication":"arXiv"},{"issue":"4","abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1256303,"file_name":"2019_GBE_Huylmans.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_id":"6446","relation":"main_file"}],"oa_version":"Published Version","_id":"6418","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 11","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","ddc":["570"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-04-01T00:00:00Z","citation":{"ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044."},"publication":"Genome biology and evolution","page":"1033-1044","ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"record":[{"id":"6060","status":"public","relation":"popular_science"}]},"author":[{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"volume":11,"date_updated":"2024-02-21T12:45:41Z","date_created":"2019-05-13T07:58:38Z","year":"2019","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","publication_status":"published","publication_identifier":{"eissn":["1759-6653"]},"month":"04","doi":"10.1093/gbe/evz053","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000476569800003"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"citation":{"ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","short":"I. Tomanek, (2019)."},"oa":1,"date_published":"2019-11-13T00:00:00Z","doi":"10.15479/AT:ISTA:7016","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"has_accepted_license":"1","article_processing_charge":"No","day":"13","month":"11","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"status":"public","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","ddc":["576"],"year":"2019","_id":"7016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"itomanek","file_size":2456192500,"content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_name":"D8_S35_R2_001.fastq","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-13T08:52:21Z","checksum":"72441055043eda4cbf1398a422e2c118","file_id":"7017","title":"Locus1_amplified","relation":"main_file"},{"file_size":2833452234,"content_type":"application/octet-stream","creator":"itomanek","access_level":"open_access","description":"Illumina whole genome sequence data for Locus 1 - 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However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature."}],"file_date_updated":"2020-07-14T12:47:47Z"},{"date_published":"2019-12-06T00:00:00Z","doi":"10.15479/AT:ISTA:7154","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154","ista":"Guseinov R. 2019. 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","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6060","year":"2019","date_created":"2019-02-28T10:55:15Z","date_updated":"2024-02-21T12:45:42Z","file":[{"creator":"bvicoso","file_size":36646050,"content_type":"application/zip","file_name":"SupData.zip","access_level":"open_access","date_created":"2019-02-28T10:54:27Z","date_updated":"2020-07-14T12:47:17Z","checksum":"a338a622d728af0e3199cb07e6dd64d3","file_id":"6061","relation":"main_file"}],"oa_version":"Published Version","author":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6418","status":"public","relation":"research_paper"}]},"type":"research_data","file_date_updated":"2020-07-14T12:47:17Z","oa":1,"citation":{"ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","short":"B. Vicoso, (2019).","mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060."},"date_published":"2019-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:6060","month":"02","day":"28","article_processing_charge":"No","has_accepted_license":"1"},{"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"_id":"6074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","date_updated":"2024-02-21T13:41:01Z","date_created":"2019-03-07T13:32:35Z","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/zip","file_size":33202743,"file_name":"Setd5_paper.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_id":"6084","relation":"supplementary_material"}],"author":[{"last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"3","status":"public","relation":"research_paper"}]},"type":"research_data","file_date_updated":"2020-07-14T12:47:18Z","abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"citation":{"mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019).","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019."},"oa":1,"date_published":"2019-01-09T00:00:00Z","doi":"10.15479/AT:ISTA:6074","day":"09","month":"01","article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2019-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:6062","citation":{"chicago":"Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062.","short":"M. Nardin, (2019).","mla":"Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062.","apa":"Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062","ieee":"M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.","ista":"Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062.","ama":"Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062"},"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"day":"29","month":"03","article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"6194"}]},"date_created":"2019-03-04T14:20:58Z","date_updated":"2024-02-21T12:46:04Z","oa_version":"Published Version","file":[{"file_size":37002186,"content_type":"application/zip","creator":"mnardin","access_level":"open_access","file_name":"Online_data.zip","checksum":"48e7b9a02939b763417733239522a236","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-05T09:29:37Z","relation":"main_file","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_id":"6068"}],"_id":"6062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","status":"public","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:18Z","abstract":[{"text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7).","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","type":"research_data"},{"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"oa":1,"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"month":"03","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","volume":36,"author":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5757"}]},"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2019","pmid":1,"date_published":"2019-03-01T00:00:00Z","page":"500-515","publication":"Molecular biology and evolution","citation":{"short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","intvolume":" 36","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6089","abstract":[{"lang":"eng","text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general."}],"issue":"3","type":"journal_article"},{"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th6179","month":"03","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"year":"2019","date_updated":"2024-02-22T14:34:33Z","date_created":"2019-03-28T08:58:59Z","author":[{"last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1144"},{"status":"public","relation":"part_of_dissertation","id":"6186"},{"id":"6185","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6182"},{"id":"1012","relation":"part_of_dissertation","status":"public"},{"id":"6184","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2020-07-14T12:47:21Z","ec_funded":1,"page":"375","citation":{"ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","apa":"Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179","mla":"Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.","chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179."},"date_published":"2019-03-18T00:00:00Z","day":"18","article_processing_charge":"No","has_accepted_license":"1","title":"From Dyson to Pearcey: Universal statistics in random matrix theory","ddc":["515","519"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6179","oa_version":"Published Version","file":[{"creator":"dernst","file_size":7104482,"content_type":"application/x-gzip","file_name":"2019_Schroeder_Thesis.tar.gz","access_level":"closed","date_created":"2019-03-28T08:53:52Z","date_updated":"2020-07-14T12:47:21Z","checksum":"6926f66f28079a81c4937e3764be00fc","file_id":"6180","relation":"source_file"},{"file_name":"2019_Schroeder_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4228794,"creator":"dernst","relation":"main_file","file_id":"6181","date_updated":"2020-07-14T12:47:21Z","date_created":"2019-03-28T08:53:52Z","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal 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. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure."}]},{"publication_identifier":{"issn":["0302-9743"],"isbn":["9783030129385","9783030129392"],"eissn":["1611-3349"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-12939-2_18","conference":{"location":"Stuttgart, Germany","start_date":"2018-10-09","end_date":"2018-10-12","name":"GCPR: Conference on Pattern Recognition"},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1804.04171"]},"ec_funded":1,"volume":11269,"date_updated":"2024-02-22T14:57:29Z","date_created":"2019-05-24T09:48:36Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"6944"}]},"author":[{"full_name":"Sun, Rémy","last_name":"Sun","first_name":"Rémy"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"department":[{"_id":"ChLa"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2019-02-14T00:00:00Z","page":"244-259","citation":{"chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-12939-2_18.","mla":"Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:10.1007/978-3-030-12939-2_18.","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","ista":"Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.","apa":"Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-12939-2_18","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18"},"abstract":[{"text":"Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. ","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 11269","status":"public","title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","_id":"6482","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"type":"conference","abstract":[{"lang":"eng","text":"We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6642","title":"On diffusive variants of some classical viscoelastic rate-type models","status":"public","intvolume":" 2107","oa_version":"Preprint","scopus_import":"1","day":"21","article_processing_charge":"No","publication":"AIP Conference Proceedings","citation":{"mla":"Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing, 2019, doi:10.1063/1.5109493.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","chicago":"Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings, Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.","ama":"Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing; 2019. doi:10.1063/1.5109493","ista":"Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference on Novel Trends in Rheology vol. 2107, 020002.","apa":"Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of some classical viscoelastic rate-type models. In AIP Conference Proceedings (Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493","ieee":"M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech Republic, 2019, vol. 2107."},"date_published":"2019-05-21T00:00:00Z","article_number":"020002","year":"2019","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"AIP Publishing","author":[{"full_name":"Dostalík, Mark","last_name":"Dostalík","first_name":"Mark"},{"first_name":"Vít","last_name":"Pruša","full_name":"Pruša, Vít"},{"last_name":"Skrivan","first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas"}],"date_updated":"2024-02-28T13:01:28Z","date_created":"2019-07-15T10:07:09Z","volume":2107,"month":"05","oa":1,"external_id":{"arxiv":["1902.07983"],"isi":["000479303100002"]},"main_file_link":[{"url":"https://arxiv.org/abs/1902.07983","open_access":"1"}],"quality_controlled":"1","isi":1,"conference":{"end_date":"2019-07-31","start_date":"2019-07-30","location":"Zlin, Czech Republic","name":"8th International Conference on Novel Trends in Rheology"},"doi":"10.1063/1.5109493","language":[{"iso":"eng"}]},{"month":"12","publication_identifier":{"issn":["00222488"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000505529800002"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.5138135","article_number":"123504","file_date_updated":"2020-07-14T12:47:54Z","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","year":"2019","date_created":"2020-01-05T23:00:46Z","date_updated":"2024-02-28T13:01:45Z","volume":60,"author":[{"full_name":"Jaksic, Vojkan","first_name":"Vojkan","last_name":"Jaksic"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"letter_note","publication":"Journal of Mathematical Physics","citation":{"ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 2019;60(12). doi:10.1063/1.5138135","ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics, vol. 60, no. 12. AIP Publishing, 2019.","apa":"Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.5138135","ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.","chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135."},"date_published":"2019-12-01T00:00:00Z","type":"journal_article","issue":"12","title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","status":"public","ddc":["500"],"intvolume":" 60","_id":"7226","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"7244","relation":"main_file","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:59:13Z","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","file_name":"2019_JournalMathPhysics_Jaksic.pdf","access_level":"open_access","creator":"dernst","file_size":1025015,"content_type":"application/pdf"}]},{"day":"16","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Physical Review Research","citation":{"short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:10.1103/physrevresearch.1.033177.","chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research. American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177","apa":"Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” Physical Review Research, vol. 1, no. 3. American Physical Society, 2019.","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177."},"date_published":"2019-12-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"issue":"3","status":"public","title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","ddc":["530"],"intvolume":" 1","_id":"7190","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"7193","relation":"main_file","checksum":"382eb67e62a77052a23887332d363f96","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-18T07:13:14Z","access_level":"open_access","file_name":"2019_PhysRevResearch_Huber.pdf","creator":"dernst","file_size":1370022,"content_type":"application/pdf"}],"oa_version":"Published Version","month":"12","publication_identifier":{"issn":["2643-1564"]},"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1908.02483"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.1.033177","article_number":"033177","file_date_updated":"2020-07-14T12:47:52Z","ec_funded":1,"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2019","date_updated":"2024-02-28T13:11:40Z","date_created":"2019-12-17T13:03:41Z","volume":1,"author":[{"full_name":"Huber, D.","last_name":"Huber","first_name":"D."},{"full_name":"Hammer, H.-W.","last_name":"Hammer","first_name":"H.-W."},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"}]},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000470885800005"],"arxiv":["1812.05561"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.05561"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.122.220603","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"month":"06","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","year":"2019","volume":122,"date_created":"2019-06-23T21:59:13Z","date_updated":"2024-02-28T13:12:22Z","author":[{"first_name":"Soonwon","last_name":"Choi","full_name":"Choi, Soonwon"},{"full_name":"Turner, Christopher J.","last_name":"Turner","first_name":"Christopher J."},{"full_name":"Pichler, Hannes","first_name":"Hannes","last_name":"Pichler"},{"last_name":"Ho","first_name":"Wen Wei","full_name":"Ho, Wen Wei"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Lukin, Mikhail D.","first_name":"Mikhail D.","last_name":"Lukin"},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."}],"article_number":"220603","article_type":"original","citation":{"chicago":"Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603.","mla":"Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.220603.","short":"S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn, M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).","ista":"Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 122(22), 220603.","ieee":"S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society, 2019.","apa":"Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z., … Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603","ama":"Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603"},"publication":"Physical Review Letters","date_published":"2019-06-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"07","intvolume":" 122","status":"public","title":"Emergent SU(2) dynamics and perfect quantum many-body scars","_id":"6575","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"22","abstract":[{"lang":"eng","text":"Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit."}]},{"abstract":[{"text":"In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6092","title":"Quantum many-body dynamics of the Einstein-de Haas effect","status":"public","intvolume":" 99","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","publication":"Physical Review B","citation":{"ieee":"J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American Physical Society, 2019.","apa":"Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.99.064428","ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","ama":"Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428","chicago":"Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428.","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","mla":"Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:10.1103/PhysRevB.99.064428."},"article_number":"064428","author":[{"full_name":"Mentink, Johann H","first_name":"Johann H","last_name":"Mentink"},{"first_name":"Mikhail","last_name":"Katsnelson","full_name":"Katsnelson, Mikhail"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:11:54Z","volume":99,"year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"month":"02","doi":"10.1103/PhysRevB.99.064428","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"external_id":{"isi":["000459223400004"],"arxiv":["1802.01638"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}]},{"scopus_import":"1","day":"26","article_processing_charge":"No","publication":"Physical Review E","citation":{"ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423."},"date_published":"2019-02-26T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing."}],"issue":"2","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","intvolume":" 99","oa_version":"Preprint","month":"02","oa":1,"external_id":{"isi":["000459916500007"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevE.99.022423","language":[{"iso":"eng"}],"article_number":"022423","year":"2019","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","author":[{"full_name":"Carballo-Pacheco, Martín","last_name":"Carballo-Pacheco","first_name":"Martín"},{"full_name":"Desponds, Jonathan","last_name":"Desponds","first_name":"Jonathan"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"first_name":"Andreas","last_name":"Mayer","full_name":"Mayer, Andreas"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reddy, Gautam","last_name":"Reddy","first_name":"Gautam"},{"full_name":"Nemenman, Ilya","first_name":"Ilya","last_name":"Nemenman"},{"last_name":"Mora","first_name":"Thierry","full_name":"Mora, Thierry"}],"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","volume":99},{"day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-05-08T00:00:00Z","article_type":"original","publication":"Physical Review X","citation":{"ieee":"C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026.","short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026."},"abstract":[{"text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations.","lang":"eng"}],"issue":"2","type":"journal_article","file":[{"checksum":"065ff82ee4a1d2c3773ce4b76ff4213c","date_created":"2019-08-12T12:14:18Z","date_updated":"2020-07-14T12:47:40Z","file_id":"6802","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1193550,"access_level":"open_access","file_name":"2019_PhysReviewX_Hubert.pdf"}],"oa_version":"Published Version","status":"public","ddc":["530"],"title":"Attractive dipolar coupling between stacked exciton fluids","intvolume":" 9","_id":"6786","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"eissn":["2160-3308"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevX.9.021026","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1807.11238"],"isi":["000467402900001"]},"oa":1,"file_date_updated":"2020-07-14T12:47:40Z","article_number":"021026","date_created":"2019-08-11T21:59:20Z","date_updated":"2024-02-28T13:12:48Z","volume":9,"author":[{"first_name":"Colin","last_name":"Hubert","full_name":"Hubert, Colin"},{"full_name":"Baruchi, Yifat","last_name":"Baruchi","first_name":"Yifat"},{"last_name":"Mazuz-Harpaz","first_name":"Yotam","full_name":"Mazuz-Harpaz, Yotam"},{"first_name":"Kobi","last_name":"Cohen","full_name":"Cohen, Kobi"},{"full_name":"Biermann, Klaus","first_name":"Klaus","last_name":"Biermann"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"first_name":"Ken","last_name":"West","full_name":"West, Ken"},{"last_name":"Pfeiffer","first_name":"Loren","full_name":"Pfeiffer, Loren"},{"first_name":"Ronen","last_name":"Rapaport","full_name":"Rapaport, Ronen"},{"full_name":"Santos, Paulo","first_name":"Paulo","last_name":"Santos"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2019"},{"publication":"Physical Review B","citation":{"mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504.","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504","ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","apa":"Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019."},"article_type":"original","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7013","status":"public","title":"Probing the many-body localization phase transition with superconducting circuits","intvolume":" 100","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition."}],"issue":"13","external_id":{"isi":["000489036500004"],"arxiv":["1907.04043"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.04043","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1103/physrevb.100.134504","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"author":[{"full_name":"Orell, Tuure","last_name":"Orell","first_name":"Tuure"},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"full_name":"Silveri, Matti","last_name":"Silveri","first_name":"Matti"}],"date_updated":"2024-02-28T13:13:13Z","date_created":"2019-11-13T08:25:48Z","volume":100,"article_number":"134504"},{"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1907.13579","open_access":"1"}],"oa":1,"external_id":{"isi":["000498845700006"],"arxiv":["1907.13579"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.100.174518","month":"11","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","year":"2019","date_updated":"2024-02-28T13:14:08Z","date_created":"2019-12-22T23:00:41Z","volume":100,"author":[{"full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","first_name":"Pietro","last_name":"Brighi"},{"last_name":"Grilli","first_name":"Marco","full_name":"Grilli, Marco"},{"first_name":"Brigitte","last_name":"Leridon","full_name":"Leridon, Brigitte"},{"full_name":"Caprara, Sergio","first_name":"Sergio","last_name":"Caprara"}],"article_number":"174518","article_type":"original","publication":"Physical Review B","citation":{"mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.100.174518.","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518.","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” Physical Review B, vol. 100, no. 17. American Physical Society, 2019.","apa":"Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518"},"date_published":"2019-11-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"No","status":"public","title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","intvolume":" 100","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7200","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario).","lang":"eng"}],"issue":"17"},{"language":[{"iso":"eng"}],"doi":"10.1103/physreve.100.013112","isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"oa":1,"external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.05860"}],"month":"07","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"date_updated":"2024-02-28T13:13:00Z","date_created":"2019-08-09T09:40:41Z","volume":100,"author":[{"full_name":"Suri, Balachandra","last_name":"Suri","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pallantla","first_name":"Ravi Kumar","full_name":"Pallantla, Ravi Kumar"},{"full_name":"Schatz, Michael F.","first_name":"Michael F.","last_name":"Schatz"},{"last_name":"Grigoriev","first_name":"Roman O.","full_name":"Grigoriev, Roman O."}],"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","year":"2019","ec_funded":1,"article_number":"013112","date_published":"2019-07-25T00:00:00Z","article_type":"original","publication":"Physical Review E","citation":{"short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112.","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019.","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112."},"day":"25","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","ddc":["532"],"intvolume":" 100","_id":"6779","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace."}],"issue":"1","type":"journal_article"}]