[{"_id":"11711","publisher":"Zenodo","article_processing_charge":"No","day":"06","related_material":{"record":[{"relation":"used_in_publication","id":"11704","status":"public"}]},"citation":{"apa":"Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","short":"N.B. Budanur, (2022).","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>","chicago":"Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6802720\">https://doi.org/10.5281/ZENODO.6802720</a>.","ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","mla":"Budanur, Nazmi B. <i>Burakbudanur/Autoacc-Public</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>."},"department":[{"_id":"BjHo"}],"abstract":[{"text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\"","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"burakbudanur/autoacc-public","type":"research_data_reference","date_created":"2022-08-01T08:06:33Z","status":"public","author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"07","corr_author":"1","ddc":["000"],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.6802720","open_access":"1"}],"year":"2022","doi":"10.5281/ZENODO.6802720","date_published":"2022-07-06T00:00:00Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"oa_version":"Published Version","date_updated":"2025-06-11T13:37:36Z"},{"month":"05","corr_author":"1","ddc":["570"],"oa":1,"article_type":"letter_note","doi":"10.1186/s13104-022-06061-9","author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela","last_name":"Nikolic"},{"first_name":"Martina","last_name":"Sauert","full_name":"Sauert, Martina"},{"full_name":"Albanese, Tanino G.","last_name":"Albanese","first_name":"Tanino G."},{"last_name":"Moll","full_name":"Moll, Isabella","first_name":"Isabella"}],"license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2022-05-13T00:00:00Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-04-14T09:24:53Z","article_number":"173","external_id":{"pmid":["35562780"]},"scopus_import":"1","language":[{"iso":"eng"}],"project":[{"_id":"26956E74-B435-11E9-9278-68D0E5697425","name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","grant_number":"V00738","call_identifier":"FWF"}],"day":"13","publication_identifier":{"issn":["1756-0500"]},"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We acknowledge the Max Perutz Labs FACS Facility together with Thomas Sauer. NN is grateful to Călin C. Guet for his support.\r\nThis work was funded by the Elise Richter grant V738 of the Austrian Science Fund (FWF), and the FWF Lise Meitner grant M1697, to NN; and by the FWF grant P22249, FWF Special Research Program RNA-REG F43 (subproject F4316), and FWF doctoral program RNA Biology (W1207), to IM. Open access funding provided by the Austrian Science Fund.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"BMC Research Notes","date_created":"2022-08-01T09:04:27Z","citation":{"ieee":"N. Nikolic, M. Sauert, T. G. Albanese, and I. Moll, “Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli,” <i>BMC Research Notes</i>, vol. 15. Springer Nature, 2022.","chicago":"Nikolic, Nela, Martina Sauert, Tanino G. Albanese, and Isabella Moll. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>.","ista":"Nikolic N, Sauert M, Albanese TG, Moll I. 2022. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Research Notes. 15, 173.","short":"N. Nikolic, M. Sauert, T.G. Albanese, I. Moll, BMC Research Notes 15 (2022).","ama":"Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. 2022;15. doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>","apa":"Nikolic, N., Sauert, M., Albanese, T. G., &#38; Moll, I. (2022). Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. <i>BMC Research Notes</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13104-022-06061-9\">https://doi.org/10.1186/s13104-022-06061-9</a>","mla":"Nikolic, Nela, et al. “Quantifying Heterologous Gene Expression during Ectopic MazF Production in Escherichia Coli.” <i>BMC Research Notes</i>, vol. 15, 173, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13104-022-06061-9\">10.1186/s13104-022-06061-9</a>."},"year":"2022","intvolume":"        15","status":"public","file":[{"relation":"main_file","file_name":"2022_BMCResearchNotes_Nikolic.pdf","creator":"dernst","date_updated":"2022-08-01T09:24:42Z","date_created":"2022-08-01T09:24:42Z","content_type":"application/pdf","checksum":"008156e5340e9789f0f6d82bde4d347a","access_level":"open_access","success":1,"file_size":1545310,"file_id":"11714"}],"volume":15,"has_accepted_license":"1","pmid":1,"file_date_updated":"2022-08-01T09:24:42Z","article_processing_charge":"No","_id":"11713","quality_controlled":"1","abstract":[{"lang":"eng","text":"Objective: MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA).\r\nResults: Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes."}],"title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","type":"journal_article","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13104-022-06152-7"}]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"department":[{"_id":"CaGu"}]},{"citation":{"mla":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>, vol. 408, no. Part A, 108591, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>.","chicago":"Drach, Kostiantyn, and Dierk Schleicher. “Rigidity of Newton Dynamics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>.","ista":"Drach K, Schleicher D. 2022. Rigidity of Newton dynamics. Advances in Mathematics. 408(Part A), 108591.","short":"K. Drach, D. Schleicher, Advances in Mathematics 408 (2022).","ama":"Drach K, Schleicher D. Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. 2022;408(Part A). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108591\">10.1016/j.aim.2022.108591</a>","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022.","apa":"Drach, K., &#38; Schleicher, D. (2022). Rigidity of Newton dynamics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108591\">https://doi.org/10.1016/j.aim.2022.108591</a>"},"date_created":"2022-08-01T17:08:16Z","publication":"Advances in Mathematics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We are grateful to a number of colleagues for helpful and inspiring discussions during the time when we worked on this project, in particular Dima Dudko, Misha Hlushchanka, John Hubbard, Misha Lyubich, Oleg Kozlovski, and Sebastian van Strien. Finally, we would like to thank our dynamics research group for numerous helpful and enjoyable discussions: Konstantin Bogdanov, Roman Chernov, Russell Lodge, Steffen Maaß, David Pfrang, Bernhard Reinke, Sergey Shemyakov, and Maik Sowinski. We gratefully acknowledge support by the Advanced Grant “HOLOGRAM” (#695 621) of the European Research Council (ERC), as well as hospitality of Cornell University in the spring of 2018 while much of this work was prepared. The first-named author also acknowledges the support of the ERC Advanced Grant “SPERIG” (#885 707).","publisher":"Elsevier","publication_status":"published","publication_identifier":{"issn":["0001-8708"]},"day":"29","project":[{"name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707","call_identifier":"H2020"}],"scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000860924200005"]},"article_number":"108591","date_updated":"2025-04-14T07:53:45Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2022-10-29T00:00:00Z","author":[{"last_name":"Drach","full_name":"Drach, Kostiantyn","first_name":"Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115","orcid":"0000-0002-9156-8616"},{"first_name":"Dierk","last_name":"Schleicher","full_name":"Schleicher, Dierk"}],"doi":"10.1016/j.aim.2022.108591","article_type":"original","oa":1,"ddc":["510"],"corr_author":"1","month":"10","department":[{"_id":"VaKa"}],"isi":1,"keyword":["General Mathematics"],"type":"journal_article","title":"Rigidity of Newton dynamics","abstract":[{"lang":"eng","text":"We study rigidity of rational maps that come from Newton's root finding method for polynomials of arbitrary degrees. We establish dynamical rigidity of these maps: each point in the Julia set of a Newton map is either rigid (i.e. its orbit can be distinguished in combinatorial terms from all other orbits), or the orbit of this point eventually lands in the filled-in Julia set of a polynomial-like restriction of the original map. As a corollary, we show that the Julia sets of Newton maps in many non-trivial cases are locally connected; in particular, every cubic Newton map without Siegel points has locally connected Julia set.\r\nIn the parameter space of Newton maps of arbitrary degree we obtain the following rigidity result: any two combinatorially equivalent Newton maps are quasiconformally conjugate in a neighborhood of their Julia sets provided that they either non-renormalizable, or they are both renormalizable “in the same way”.\r\nOur main tool is a generalized renormalization concept called “complex box mappings” for which we extend a dynamical rigidity result by Kozlovski and van Strien so as to include irrationally indifferent and renormalizable situations."}],"quality_controlled":"1","_id":"11717","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2023-02-02T07:39:09Z","issue":"Part A","has_accepted_license":"1","volume":408,"file":[{"file_name":"2022_AdvancesMathematics_Drach.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2023-02-02T07:39:09Z","date_created":"2023-02-02T07:39:09Z","creator":"dernst","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","access_level":"open_access","success":1,"file_size":2164036,"file_id":"12474"}],"status":"public","intvolume":"       408","year":"2022","ec_funded":1},{"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"isi":1,"keyword":["Multidisciplinary"],"type":"journal_article","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","abstract":[{"text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term.","lang":"eng"}],"quality_controlled":"1","_id":"11723","article_processing_charge":"No","file_date_updated":"2022-08-08T07:42:09Z","pmid":1,"issue":"31","has_accepted_license":"1","volume":119,"file":[{"date_created":"2022-08-08T07:42:09Z","creator":"dernst","date_updated":"2022-08-08T07:42:09Z","content_type":"application/pdf","relation":"main_file","file_name":"2022_PNAS_Li.pdf","success":1,"access_level":"open_access","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_id":"11747","file_size":2506262}],"status":"public","intvolume":"       119","year":"2022","citation":{"mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>"},"date_created":"2022-08-04T20:06:49Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","publication_status":"published","publisher":"National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"day":"25","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351"}],"language":[{"iso":"eng"}],"scopus_import":"1","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"article_number":"e2121058119","date_updated":"2025-05-14T11:01:00Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2022-07-25T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"first_name":"Lanxin","full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","full_name":"Chen, Huihuang","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f"},{"first_name":"Saqer S.","full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"last_name":"Adamowski","full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1073/pnas.2121058119","article_type":"original","ddc":["580"],"oa":1,"month":"07","corr_author":"1"},{"issue":"31","has_accepted_license":"1","volume":119,"file_date_updated":"2022-08-08T07:31:19Z","pmid":1,"year":"2022","intvolume":"       119","status":"public","file":[{"success":1,"checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","access_level":"open_access","file_id":"11745","file_size":1001164,"creator":"dernst","date_updated":"2022-08-08T07:31:19Z","date_created":"2022-08-08T07:31:19Z","content_type":"application/pdf","relation":"main_file","file_name":"2022_PNAS_Orliac.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies."}],"title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","isi":1,"department":[{"_id":"MaRo"}],"related_material":{"record":[{"status":"public","id":"13064","relation":"research_data"}]},"article_processing_charge":"No","_id":"11733","quality_controlled":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2025-06-12T06:22:37Z","date_published":"2022-07-29T00:00:00Z","article_number":"e2121279119","external_id":{"pmid":["35905320"],"isi":["000881496900003"]},"article_type":"original","doi":"10.1073/pnas.2121279119","month":"07","corr_author":"1","ddc":["570"],"oa":1,"author":[{"last_name":"Orliac","full_name":"Orliac, Etienne J.","first_name":"Etienne J."},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"first_name":"Sven E.","full_name":"Ojavee, Sven E.","last_name":"Ojavee"},{"first_name":"Kristi","last_name":"Läll","full_name":"Läll, Kristi"},{"first_name":"Reedik","last_name":"Mägi","full_name":"Mägi, Reedik"},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2022-08-07T22:01:56Z","acknowledgement":"This project was funded by Swiss National Science Foundation Eccellenza Grant PCEGP3-181181(toM.R.R.) and by core funding from the Institute of Science and Technology Austria. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). K.L. and R.M. were supported by the Estonian Research Council Grant PRG687. Estonian Biobank computations were performed in the High-Performance Computing Centre, University of Tartu.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Orliac, Etienne J., et al. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121279119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>.","apa":"Orliac, E. J., Trejo Banos, D., Ojavee, S. E., Läll, K., Mägi, R., Visscher, P. M., &#38; Robinson, M. R. (2022). Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>","short":"E.J. Orliac, D. Trejo Banos, S.E. Ojavee, K. Läll, R. Mägi, P.M. Visscher, M.R. Robinson, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ama":"Orliac EJ, Trejo Banos D, Ojavee SE, et al. Improving GWAS discovery and genomic prediction accuracy in biobank data. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121279119\">10.1073/pnas.2121279119</a>","chicago":"Orliac, Etienne J., Daniel Trejo Banos, Sven E. Ojavee, Kristi Läll, Reedik Mägi, Peter M. Visscher, and Matthew Richard Robinson. “Improving GWAS Discovery and Genomic Prediction Accuracy in Biobank Data.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121279119\">https://doi.org/10.1073/pnas.2121279119</a>.","ista":"Orliac EJ, Trejo Banos D, Ojavee SE, Läll K, Mägi R, Visscher PM, Robinson MR. 2022. Improving GWAS discovery and genomic prediction accuracy in biobank data. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121279119.","ieee":"E. J. Orliac <i>et al.</i>, “Improving GWAS discovery and genomic prediction accuracy in biobank data,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022."},"publication_identifier":{"eissn":["1091-6490"]},"scopus_import":"1","language":[{"iso":"eng"}],"day":"29","publication_status":"published","publisher":"National Academy of Sciences"},{"type":"journal_article","abstract":[{"text":"Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.","lang":"eng"}],"title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","isi":1,"department":[{"_id":"EvBe"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"_id":"11734","quality_controlled":"1","issue":"31","has_accepted_license":"1","volume":119,"file_date_updated":"2022-08-08T07:09:58Z","pmid":1,"year":"2022","intvolume":"       119","status":"public","file":[{"access_level":"open_access","checksum":"6e97dedc281247fc3fe238a209f14af0","success":1,"file_size":3092330,"file_id":"11744","relation":"main_file","file_name":"2022_PNAS_Abualia.pdf","content_type":"application/pdf","date_updated":"2022-08-08T07:09:58Z","date_created":"2022-08-08T07:09:58Z","creator":"dernst"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2022-08-07T22:01:57Z","acknowledgement":"We acknowledge Hana Semeradova, Juan Carlos Montesinos, Nicola Cavallari, Marc¸al Gallem\u0003ı, Kaori Tabata, Andrej Hurn\u0003y, and Sascha Waidmann for sharing materials; and Marina Borges Osorio for critical reading of the manuscript. Work in the E. Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to K.O., R.A., and E. Benkova. We acknowledge the Bioimaging Facility and Life Science Facilities of the Institute of Science\r\nand Technology Austria. We give sincere thanks to Hana Martınkova and Petra Amakorova for their help with cytokinin analyses. This work was funded by the Czech Science Foundation (Project No. 19-00973S).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Abualia R, Ötvös K, Novák O, Bouguyon E, Domanegg K, Krapp A, Nacry P, Gojon A, Lacombe B, Benková E. 2022. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2122460119.","short":"R. Abualia, K. Ötvös, O. Novák, E. Bouguyon, K. Domanegg, A. Krapp, P. Nacry, A. Gojon, B. Lacombe, E. Benková, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ama":"Abualia R, Ötvös K, Novák O, et al. Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>","chicago":"Abualia, Rashed, Krisztina Ötvös, Ondřej Novák, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, and Eva Benková. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>.","ieee":"R. Abualia <i>et al.</i>, “Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","apa":"Abualia, R., Ötvös, K., Novák, O., Bouguyon, E., Domanegg, K., Krapp, A., … Benková, E. (2022). Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122460119\">https://doi.org/10.1073/pnas.2122460119</a>","mla":"Abualia, Rashed, et al. “Molecular Framework Integrating Nitrate Sensing in Root and Auxin-Guided Shoot Adaptive Responses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2122460119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122460119\">10.1073/pnas.2122460119</a>."},"publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"day":"25","publisher":"National Academy of Sciences","publication_status":"published","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","date_updated":"2025-05-14T11:00:29Z","date_published":"2022-07-25T00:00:00Z","article_number":"e2122460119","external_id":{"pmid":["35878040"],"isi":["000881496900007"]},"article_type":"original","doi":"10.1073/pnas.2122460119","corr_author":"1","month":"07","ddc":["570"],"oa":1,"author":[{"last_name":"Abualia","full_name":"Abualia, Rashed","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"},{"orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös","full_name":"Ötvös, Krisztina"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"full_name":"Bouguyon, Eleonore","last_name":"Bouguyon","first_name":"Eleonore"},{"orcid":"0000-0002-1215-4264","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","first_name":"Kevin","last_name":"Domanegg","full_name":"Domanegg, Kevin"},{"last_name":"Krapp","full_name":"Krapp, Anne","first_name":"Anne"},{"full_name":"Nacry, Philip","last_name":"Nacry","first_name":"Philip"},{"last_name":"Gojon","full_name":"Gojon, Alain","first_name":"Alain"},{"last_name":"Lacombe","full_name":"Lacombe, Benoit","first_name":"Benoit"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"}]},{"date_published":"2022-07-22T00:00:00Z","oa_version":"Submitted Version","date_updated":"2025-04-14T07:28:57Z","article_number":"150","external_id":{"isi":["000830989200018"]},"month":"07","ddc":["000"],"oa":1,"article_type":"original","doi":"10.1145/3528223.3530071","author":[{"first_name":"Rulin","last_name":"Chen","full_name":"Chen, Rulin"},{"full_name":"Wang, Ziqi","last_name":"Wang","first_name":"Ziqi"},{"full_name":"Song, Peng","last_name":"Song","first_name":"Peng"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd"}],"acknowledgement":"We thank the reviewers for the valuable comments, David Gontier for sharing the source code of the baseline design approach, Christian Hafner for proofreading the paper, Keenan Crane for the 3D model of Cow, and Thingiverse for the 3D models of Moai and Owl. This work was supported by the SUTD Start-up Research Grant (Number: SRG ISTD 2019 148), the Swiss National Science Foundation (NCCR Digital Fabrication Agreement #51NF40-141853), and\r\nthe European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 715767 – MATERIALIZABLE).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"ACM Transactions on Graphics","date_created":"2022-08-07T22:01:57Z","citation":{"short":"R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022).","ama":"Chen R, Wang Z, Song P, Bickel B. Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>","chicago":"Chen, Rulin, Ziqi Wang, Peng Song, and Bernd Bickel. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>.","ista":"Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level interlocking puzzles. ACM Transactions on Graphics. 41(4), 150.","ieee":"R. Chen, Z. Wang, P. Song, and B. Bickel, “Computational design of high-level interlocking puzzles,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","apa":"Chen, R., Wang, Z., Song, P., &#38; Bickel, B. (2022). Computational design of high-level interlocking puzzles. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530071\">https://doi.org/10.1145/3528223.3530071</a>","mla":"Chen, Rulin, et al. “Computational Design of High-Level Interlocking Puzzles.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 150, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530071\">10.1145/3528223.3530071</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"}],"day":"22","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publication_status":"published","publisher":"Association for Computing Machinery","has_accepted_license":"1","volume":41,"issue":"4","file_date_updated":"2022-08-28T07:56:19Z","ec_funded":1,"year":"2022","intvolume":"        41","status":"public","file":[{"relation":"main_file","file_name":"Chen-2022-High-LevelPuzzle_authorVersion.pdf","date_updated":"2022-08-28T07:56:19Z","creator":"bbickel","date_created":"2022-08-28T07:56:19Z","content_type":"application/pdf","file_size":16896871,"file_id":"11992","access_level":"open_access","checksum":"0b51651be45b1b33f2072bd5d2686c69","success":1}],"abstract":[{"text":"Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.\r\n\r\nIn this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.","lang":"eng"}],"title":"Computational design of high-level interlocking puzzles","type":"journal_article","related_material":{"link":[{"url":"https://ista.ac.at/en/news/unlocking-interlocking-riddles/","relation":"press_release","description":"News on ISTA website"}]},"isi":1,"department":[{"_id":"BeBi"}],"article_processing_charge":"No","_id":"11735","quality_controlled":"1"},{"issue":"4","volume":41,"status":"public","intvolume":"        41","year":"2022","department":[{"_id":"ChWo"}],"isi":1,"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/digital-yarn-real-socks/","description":"News on the ISTA website"}],"record":[{"id":"12358","status":"public","relation":"dissertation_contains"}]},"type":"journal_article","title":"Estimation of yarn-level simulation models for production fabrics","abstract":[{"text":"This paper introduces a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compiled a database from physical tests of several different knitted fabrics used in the textile industry. These data span different types of complex knit patterns, yarn compositions, and fabric finishes, and the results demonstrate diverse physical properties like stiffness, nonlinearity, and anisotropy.\r\n\r\nWe then develop a system for approximating these mechanical responses with yarn-level cloth simulation. To do so, we introduce an efficient pipeline for converting between fabric-level data and yarn-level simulation, including a novel swatch-level approximation for speeding up computation, and some small-but-necessary extensions to yarn-level models used in computer graphics. The dataset used for this paper can be found at http://mslab.es/projects/YarnLevelFabrics.","lang":"eng"}],"quality_controlled":"1","_id":"11736","acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","external_id":{"isi":["000830989200114"]},"article_number":"65","date_updated":"2026-06-18T17:20:41Z","oa_version":"Published Version","date_published":"2022-07-22T00:00:00Z","author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Sperl, Georg","last_name":"Sperl"},{"first_name":"Rosa M.","full_name":"Sánchez-Banderas, Rosa M.","last_name":"Sánchez-Banderas"},{"full_name":"Li, Manwen","last_name":"Li","first_name":"Manwen"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan"},{"first_name":"Miguel A.","full_name":"Otaduy, Miguel A.","last_name":"Otaduy"}],"doi":"10.1145/3528223.3530167","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3528223.3530167"}],"oa":1,"ddc":["000"],"month":"07","citation":{"mla":"Sperl, Georg, et al. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 65, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>.","apa":"Sperl, G., Sánchez-Banderas, R. M., Li, M., Wojtan, C., &#38; Otaduy, M. A. (2022). Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>","ieee":"G. Sperl, R. M. Sánchez-Banderas, M. Li, C. Wojtan, and M. A. Otaduy, “Estimation of yarn-level simulation models for production fabrics,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ama":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. Estimation of yarn-level simulation models for production fabrics. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530167\">10.1145/3528223.3530167</a>","short":"G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions on Graphics 41 (2022).","ista":"Sperl G, Sánchez-Banderas RM, Li M, Wojtan C, Otaduy MA. 2022. Estimation of yarn-level simulation models for production fabrics. ACM Transactions on Graphics. 41(4), 65.","chicago":"Sperl, Georg, Rosa M. Sánchez-Banderas, Manwen Li, Chris Wojtan, and Miguel A. Otaduy. “Estimation of Yarn-Level Simulation Models for Production Fabrics.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530167\">https://doi.org/10.1145/3528223.3530167</a>."},"date_created":"2022-08-07T22:01:58Z","publication":"ACM Transactions on Graphics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We wish to thank the anonymous reviewers for their helpful comments. To develop this project, we were helped by many people both at Under Armour (Clay Dean, Randall Harward, Kyle Blakely, Craig Simile, Michael Seiz, Brooke Malone, Brittainy McFarland, Emilie Phan, Lindsey Kern, Courtney Oswald, Haley Barkley, Bob Chin, Adam Bayer, Connie Kwok, Marielle Newman, Nick Pence, Allison Hicks, Allison White, Candace Rubenstein, Jeremy Stangland, Fred Fagergren, Michael Mazzoleni, Nathaniel Berry, Manuel Frank) and SEDDI (Gabriel Cirio, Alejandro Rodríguez, Sofía Dominguez, Alicia Nicas, Elena Garcés, Daniel Rodríguez, David Pascual, Manuel Godoy, Sergio Suja, Sergio Ruiz, Roberto Condori, Alberto Martín, Graham Sullivan). We also thank the members of the Visual Computing Group at IST Austria and the Multimodal Simulation Lab at URJC for their feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing, and it was funded in part by the European Research Council (ERC Consolidator Grant 772738 TouchDesign).","publication_status":"published","publisher":"Association for Computing Machinery","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"day":"22","language":[{"iso":"eng"}],"scopus_import":"1"},{"external_id":{"isi":["000834349200010"]},"article_number":"045302","date_published":"2022-07-15T00:00:00Z","date_updated":"2023-08-03T12:38:57Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","orcid":"0000-0002-1648-0999","last_name":"Dziom","full_name":"Dziom, Uladzislau","first_name":"Uladzislau"},{"first_name":"A.","full_name":"Shuvaev, A.","last_name":"Shuvaev"},{"first_name":"J.","full_name":"Gospodarič, J.","last_name":"Gospodarič"},{"full_name":"Novik, E. G.","last_name":"Novik","first_name":"E. G."},{"first_name":"A. A.","full_name":"Dobretsova, A. A.","last_name":"Dobretsova"},{"first_name":"N. N.","last_name":"Mikhailov","full_name":"Mikhailov, N. N."},{"first_name":"Z. D.","last_name":"Kvon","full_name":"Kvon, Z. D."},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev"},{"first_name":"A.","full_name":"Pimenov, A.","last_name":"Pimenov"}],"ddc":["530"],"oa":1,"month":"07","doi":"10.1103/PhysRevB.106.045302","article_type":"original","citation":{"mla":"Dziom, Uladzislau, et al. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>, vol. 106, no. 4, 045302, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>.","ieee":"U. Dziom <i>et al.</i>, “Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells,” <i>Physical Review B</i>, vol. 106, no. 4. American Physical Society, 2022.","chicago":"Dziom, Uladzislau, A. Shuvaev, J. Gospodarič, E. G. Novik, A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, Zhanybek Alpichshev, and A. Pimenov. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>.","ista":"Dziom U, Shuvaev A, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon ZD, Alpichshev Z, Pimenov A. 2022. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. Physical Review B. 106(4), 045302.","short":"U. Dziom, A. Shuvaev, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, Z. Alpichshev, A. Pimenov, Physical Review B 106 (2022).","ama":"Dziom U, Shuvaev A, Gospodarič J, et al. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. 2022;106(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>","apa":"Dziom, U., Shuvaev, A., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov, N. N., … Pimenov, A. (2022). Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the Austrian Science Funds (W 1243, I 3456-N27, I 5539-N).","date_created":"2022-08-07T22:01:58Z","publication":"Physical Review B","publisher":"American Physical Society","publication_status":"published","day":"15","language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"file_date_updated":"2022-08-08T06:58:22Z","volume":106,"has_accepted_license":"1","issue":"4","file":[{"file_size":774455,"file_id":"11743","access_level":"open_access","checksum":"115aff9e0cde2f806cb26953d7262791","success":1,"relation":"main_file","file_name":"2022_PhysRevB_Dziom.pdf","creator":"dernst","date_created":"2022-08-08T06:58:22Z","date_updated":"2022-08-08T06:58:22Z","content_type":"application/pdf"}],"intvolume":"       106","status":"public","year":"2022","department":[{"_id":"ZhAl"}],"isi":1,"title":"Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells","abstract":[{"text":"Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like electron band structure, making it a versatile solid state platform to observe and control nontrivial electrodynamic phenomena. Here we report an observation of universal terahertz (THz) transparency determined by fine-structure constant α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating phases with topologically different electronic band structure. Using THz spectroscopy in a magnetic field we obtain direct evidence of asymmetric spin splitting of the Dirac cone. This particle-hole asymmetry facilitates optical control of edge spin currents in the quantum wells.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","_id":"11737","article_processing_charge":"No"},{"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"arxiv":1,"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"call_identifier":"FWF","grant_number":"W1245","name":"Dissipation and dispersion in nonlinear partial differential equations","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"day":"18","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","date_created":"2022-08-07T22:01:59Z","publication":"SIAM Journal on Mathematical Analysis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme grant 716117 and by the AustrianScience Fund (FWF) through grants F65 and W1245.","citation":{"apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (2022). Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>","short":"D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis 54 (2022) 4297–4333.","ama":"Forkert DL, Maas J, Portinale L. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(4):4297-4333. doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>","ista":"Forkert DL, Maas J, Portinale L. 2022. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. SIAM Journal on Mathematical Analysis. 54(4), 4297–4333.","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4. Society for Industrial and Applied Mathematics, pp. 4297–4333, 2022.","mla":"Forkert, Dominik L., et al. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4, Society for Industrial and Applied Mathematics, 2022, pp. 4297–333, doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>."},"doi":"10.1137/21M1410968","article_type":"original","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2008.10962"}],"month":"07","corr_author":"1","author":[{"first_name":"Dominik L","full_name":"Forkert, Dominik L","last_name":"Forkert","id":"35C79D68-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Portinale, Lorenzo","last_name":"Portinale","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-15T08:31:31Z","oa_version":"Preprint","date_published":"2022-07-18T00:00:00Z","external_id":{"arxiv":["2008.10962"],"isi":["000889274600001"]},"article_processing_charge":"No","quality_controlled":"1","_id":"11739","page":"4297-4333","type":"journal_article","title":"Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","abstract":[{"lang":"eng","text":"We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality."}],"department":[{"_id":"JaMa"}],"isi":1,"related_material":{"record":[{"id":"10022","status":"public","relation":"earlier_version"}]},"keyword":["Fokker--Planck equation","gradient flow","evolutionary $\\Gamma$-convergence"],"year":"2022","ec_funded":1,"status":"public","intvolume":"        54","issue":"4","volume":54},{"external_id":{"isi":["000836200300001"],"arxiv":["2005.07103"]},"article_number":"P3.27","date_published":"2022-07-29T00:00:00Z","date_updated":"2024-10-09T21:03:03Z","oa_version":"Published Version","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"author":[{"first_name":"Oliver","full_name":"Cooley, Oliver","last_name":"Cooley","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d"},{"full_name":"Del Giudice, Nicola","last_name":"Del Giudice","first_name":"Nicola"},{"first_name":"Mihyun","full_name":"Kang, Mihyun","last_name":"Kang"},{"first_name":"Philipp","last_name":"Sprüssel","full_name":"Sprüssel, Philipp"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","ddc":["510"],"oa":1,"month":"07","corr_author":"1","doi":"10.37236/10607","article_type":"original","citation":{"mla":"Cooley, Oliver, et al. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3, P3.27, Electronic Journal of Combinatorics, 2022, doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>.","apa":"Cooley, O., Del Giudice, N., Kang, M., &#38; Sprüssel, P. (2022). Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>","ieee":"O. Cooley, N. Del Giudice, M. Kang, and P. Sprüssel, “Phase transition in cohomology groups of non-uniform random simplicial complexes,” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3. Electronic Journal of Combinatorics, 2022.","chicago":"Cooley, Oliver, Nicola Del Giudice, Mihyun Kang, and Philipp Sprüssel. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2022. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>.","ista":"Cooley O, Del Giudice N, Kang M, Sprüssel P. 2022. Phase transition in cohomology groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics. 29(3), P3.27.","short":"O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics 29 (2022).","ama":"Cooley O, Del Giudice N, Kang M, Sprüssel P. Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. 2022;29(3). doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","date_created":"2022-08-07T22:01:59Z","publication":"Electronic Journal of Combinatorics","publisher":"Electronic Journal of Combinatorics","publication_status":"published","day":"29","scopus_import":"1","language":[{"iso":"eng"}],"arxiv":1,"publication_identifier":{"eissn":["1077-8926"]},"file_date_updated":"2022-08-08T06:28:52Z","volume":29,"has_accepted_license":"1","issue":"3","file":[{"file_id":"11742","file_size":1768663,"success":1,"access_level":"open_access","checksum":"057c676dcee70236aa234d4ce6138c69","date_updated":"2022-08-08T06:28:52Z","creator":"dernst","date_created":"2022-08-08T06:28:52Z","content_type":"application/pdf","file_name":"2022_ElecJournCombinatorics_Cooley.pdf","relation":"main_file"}],"status":"public","intvolume":"        29","year":"2022","department":[{"_id":"MaKw"}],"isi":1,"title":"Phase transition in cohomology groups of non-uniform random simplicial complexes","abstract":[{"lang":"eng","text":"We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].\r\nWe consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition."}],"type":"journal_article","quality_controlled":"1","_id":"11740","article_processing_charge":"No"},{"has_accepted_license":"1","file_date_updated":"2022-08-11T16:09:19Z","ec_funded":1,"year":"2022","status":"public","file":[{"creator":"pwild","date_updated":"2022-08-10T15:34:04Z","date_created":"2022-08-10T15:34:04Z","content_type":"text/x-python","file_name":"flags.py","relation":"supplementary_material","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","access_level":"open_access","file_id":"11780","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","file_size":16828},{"file_name":"lowerbound.cpp","relation":"supplementary_material","date_created":"2022-08-10T15:34:10Z","creator":"pwild","date_updated":"2022-08-10T15:34:10Z","content_type":"text/x-c++src","description":"Code for proof of Lemma 8.20 in Thesis","file_size":12226,"file_id":"11781","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","access_level":"open_access"},{"content_type":"text/x-python","creator":"pwild","date_created":"2022-08-10T15:34:17Z","date_updated":"2022-08-10T15:34:17Z","file_name":"upperbound.py","relation":"supplementary_material","access_level":"open_access","checksum":"4cf81455c49e5dec3b9b2e3980137eeb","file_id":"11782","file_size":3240,"description":"Code for proof of Proposition 7.9 in Thesis"},{"relation":"main_file","file_name":"finalthesisPascalWildPDFA.pdf","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","content_type":"application/pdf","date_updated":"2022-08-11T16:08:33Z","creator":"pwild","date_created":"2022-08-11T16:08:33Z","access_level":"open_access","checksum":"4e96575b10cbe4e0d0db2045b2847774","file_size":5086282,"file_id":"11809"},{"content_type":"application/zip","date_created":"2022-08-11T16:09:19Z","date_updated":"2022-08-11T16:09:19Z","creator":"pwild","relation":"source_file","file_name":"ThesisSubmission.zip","access_level":"closed","checksum":"92d94842a1fb6dca5808448137573b2e","file_id":"11810","file_size":18150068}],"abstract":[{"lang":"eng","text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise."}],"title":"High-dimensional expansion and crossing numbers of simplicial complexes","type":"dissertation","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"UlWa"}],"article_processing_charge":"No","page":"170","_id":"11777","date_published":"2022-08-11T00:00:00Z","oa_version":"Published Version","date_updated":"2026-04-07T14:18:26Z","supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"month":"08","corr_author":"1","ddc":["500","516","514"],"oa":1,"OA_place":"publisher","degree_awarded":"PhD","doi":"10.15479/at:ista:11777","author":[{"full_name":"Wild, Pascal","last_name":"Wild","first_name":"Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-08-10T15:51:19Z","citation":{"apa":"Wild, P. (2022). <i>High-dimensional expansion and crossing numbers of simplicial complexes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>.","ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology Austria, 2022.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology Austria.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology Austria, 2022.","mla":"Wild, Pascal. <i>High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>."},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"day":"11","publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","orcid":"0000-0002-6854-1343","last_name":"Bossmann","full_name":"Bossmann, Lea","first_name":"Lea"}],"ddc":["530"],"oa":1,"month":"06","corr_author":"1","doi":"10.1063/5.0089983","article_type":"original","external_id":{"arxiv":["2203.00730"],"isi":["000809648100002"]},"article_number":"061102","date_published":"2022-06-10T00:00:00Z","date_updated":"2025-04-14T07:43:58Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","publisher":"AIP Publishing","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"10","language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"arxiv":1,"citation":{"short":"L. Bossmann, Journal of Mathematical Physics 63 (2022).","ama":"Bossmann L. Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. 2022;63(6). doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>","chicago":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>.","ista":"Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting Bose gas. Journal of Mathematical Physics. 63(6), 061102.","ieee":"L. Bossmann, “Low-energy spectrum and dynamics of the weakly interacting Bose gas,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6. AIP Publishing, 2022.","apa":"Bossmann, L. (2022). Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>","mla":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6, 061102, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"The author thanks Nataˇsa Pavlovic, Sören Petrat, Peter Pickl, Robert Seiringer, and Avy Soffer for the collaboration on Refs. 1, 2 and 21. Funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skℓodowska-Curie Grant Agreement\r\nNo. 754411 is gratefully acknowledged.","date_created":"2022-08-11T06:37:52Z","publication":"Journal of Mathematical Physics","file":[{"relation":"main_file","file_name":"2022_JourMathPhysics_Bossmann.pdf","date_updated":"2022-08-11T07:03:02Z","creator":"dernst","date_created":"2022-08-11T07:03:02Z","content_type":"application/pdf","access_level":"open_access","checksum":"d0d32c338c1896680174be88c70968fa","success":1,"file_size":5957888,"file_id":"11784"}],"intvolume":"        63","status":"public","ec_funded":1,"year":"2022","file_date_updated":"2022-08-11T07:03:02Z","volume":63,"has_accepted_license":"1","issue":"6","quality_controlled":"1","_id":"11783","article_processing_charge":"Yes (via OA deal)","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"department":[{"_id":"RoSe"}],"isi":1,"title":"Low-energy spectrum and dynamics of the weakly interacting Bose gas","abstract":[{"text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix.","lang":"eng"}],"type":"journal_article"},{"day":"28","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","date_created":"2022-08-14T22:01:45Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ieee":"Z. Toprakcioglu <i>et al.</i>, “Adsorption free energy predicts amyloid protein nucleation rates,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>","ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119.","chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>.","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2109718119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>."},"ddc":["570"],"oa":1,"month":"07","doi":"10.1073/pnas.2109718119","article_type":"original","author":[{"full_name":"Toprakcioglu, Zenon","last_name":"Toprakcioglu","first_name":"Zenon"},{"first_name":"Ayaka","full_name":"Kamada, Ayaka","last_name":"Kamada"},{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"first_name":"Mengqi","last_name":"Xie","full_name":"Xie, Mengqi"},{"first_name":"Johannes","last_name":"Krausser","full_name":"Krausser, Johannes"},{"full_name":"Wei, Jiapeng","last_name":"Wei","first_name":"Jiapeng"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."}],"date_published":"2022-07-28T00:00:00Z","date_updated":"2025-06-12T06:21:34Z","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"external_id":{"pmid":["35901206"],"isi":["000903753500002"]},"article_number":"e2109718119","article_processing_charge":"No","quality_controlled":"1","_id":"11841","title":"Adsorption free energy predicts amyloid protein nucleation rates","abstract":[{"text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.","lang":"eng"}],"type":"journal_article","department":[{"_id":"AnSa"}],"isi":1,"ec_funded":1,"year":"2022","file":[{"checksum":"0fe3878896cbeb6c44e29222ec2f336a","access_level":"open_access","success":1,"file_size":2476021,"file_id":"14386","relation":"main_file","file_name":"2022_PNAS_Toprakcioglu.pdf","date_updated":"2023-10-04T09:05:44Z","date_created":"2023-10-04T09:05:44Z","creator":"dernst","content_type":"application/pdf"}],"status":"public","intvolume":"       119","volume":119,"has_accepted_license":"1","issue":"31","pmid":1,"file_date_updated":"2023-10-04T09:05:44Z"},{"article_number":"93","external_id":{"isi":["000834834300001"],"arxiv":["2112.11154"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_updated":"2026-04-07T13:28:13Z","date_published":"2022-08-01T00:00:00Z","author":[{"first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"id":"25647992-AA84-11E9-9D75-8427E6697425","first_name":"Alice","full_name":"Marveggio, Alice","last_name":"Marveggio"}],"article_type":"original","doi":"10.1007/s00021-022-00722-2","corr_author":"1","month":"08","ddc":["510"],"oa":1,"citation":{"ieee":"S. Hensel and A. Marveggio, “Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities,” <i>Journal of Mathematical Fluid Mechanics</i>, vol. 24, no. 3. Springer Nature, 2022.","short":"S. Hensel, A. Marveggio, Journal of Mathematical Fluid Mechanics 24 (2022).","chicago":"Hensel, Sebastian, and Alice Marveggio. “Weak-Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Ninety Degree Contact Angle and Same Viscosities.” <i>Journal of Mathematical Fluid Mechanics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00021-022-00722-2\">https://doi.org/10.1007/s00021-022-00722-2</a>.","ista":"Hensel S, Marveggio A. 2022. Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities. Journal of Mathematical Fluid Mechanics. 24(3), 93.","ama":"Hensel S, Marveggio A. Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities. <i>Journal of Mathematical Fluid Mechanics</i>. 2022;24(3). doi:<a href=\"https://doi.org/10.1007/s00021-022-00722-2\">10.1007/s00021-022-00722-2</a>","apa":"Hensel, S., &#38; Marveggio, A. (2022). Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities. <i>Journal of Mathematical Fluid Mechanics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00021-022-00722-2\">https://doi.org/10.1007/s00021-022-00722-2</a>","mla":"Hensel, Sebastian, and Alice Marveggio. “Weak-Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Ninety Degree Contact Angle and Same Viscosities.” <i>Journal of Mathematical Fluid Mechanics</i>, vol. 24, no. 3, 93, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s00021-022-00722-2\">10.1007/s00021-022-00722-2</a>."},"publication":"Journal of Mathematical Fluid Mechanics","date_created":"2022-08-14T22:01:45Z","acknowledgement":"The authors warmly thank their former resp. current PhD advisor Julian Fischer for the suggestion of this problem and for valuable initial discussions on the subjects of this paper. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819) , and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","publication_status":"published","arxiv":1,"publication_identifier":{"eissn":["1422-6952"],"issn":["1422-6928"]},"scopus_import":"1","language":[{"iso":"eng"}],"day":"01","project":[{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"file_date_updated":"2022-08-16T06:55:22Z","issue":"3","volume":24,"has_accepted_license":"1","status":"public","intvolume":"        24","file":[{"content_type":"application/pdf","date_created":"2022-08-16T06:55:22Z","date_updated":"2022-08-16T06:55:22Z","creator":"cchlebak","file_name":"2022_JMathFluidMech_Hensel.pdf","relation":"main_file","file_id":"11848","file_size":2045570,"success":1,"access_level":"open_access","checksum":"75c5f286300e6f0539cf57b4dba108d5"}],"year":"2022","ec_funded":1,"isi":1,"department":[{"_id":"JuFi"}],"related_material":{"record":[{"status":"public","id":"14587","relation":"dissertation_contains"}]},"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the flow of two viscous and incompressible fluids within a bounded domain modeled by means of a two-phase Navier–Stokes system. The two fluids are assumed to be immiscible, meaning that they are separated by an interface. With respect to the motion of the interface, we consider pure transport by the fluid flow. Along the boundary of the domain, a complete slip boundary condition for the fluid velocities and a constant ninety degree contact angle condition for the interface are assumed. In the present work, we devise for the resulting evolution problem a suitable weak solution concept based on the framework of varifolds and establish as the main result a weak-strong uniqueness principle in 2D. The proof is based on a relative entropy argument and requires a non-trivial further development of ideas from the recent work of Fischer and the first author (Arch. Ration. Mech. Anal. 236, 2020) to incorporate the contact angle condition. To focus on the effects of the necessarily singular geometry of the evolving fluid domains, we work for simplicity in the regime of same viscosities for the two fluids."}],"title":"Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities","_id":"11842","quality_controlled":"1","article_processing_charge":"No"},{"_id":"11844","quality_controlled":"1","page":"246-256","article_processing_charge":"Yes (via OA deal)","isi":1,"department":[{"_id":"DaAl"}],"related_material":{"record":[{"relation":"later_version","id":"19969","status":"public"}]},"type":"conference","abstract":[{"text":"In the stochastic population protocol model, we are given a connected graph with n nodes, and in every time step, a scheduler samples an edge of the graph uniformly at random and the nodes connected by this edge interact. A fundamental task in this model is stable leader election, in which all nodes start in an identical state and the aim is to reach a configuration in which (1) exactly one node is elected as leader and (2) this node remains as the unique leader no matter what sequence of interactions follows. On cliques, the complexity of this problem has recently been settled: time-optimal protocols stabilize in Θ(n log n) expected steps using Θ(log log n) states, whereas protocols that use O(1) states require Θ(n2) expected steps.\r\n\r\nIn this work, we investigate the complexity of stable leader election on general graphs. We provide the first non-trivial time lower bounds for leader election on general graphs, showing that, when moving beyond cliques, the complexity landscape of leader election becomes very diverse: the time required to elect a leader can range from O(1) to Θ(n3) expected steps. On the upper bound side, we first observe that there exists a protocol that is time-optimal on many graph families, but uses polynomially-many states. In contrast, we give a near-time-optimal protocol that uses only O(log2n) states that is at most a factor log n slower. Finally, we show that the constant-state protocol of Beauquier et al. [OPODIS 2013] is at most a factor n log n slower than the fast polynomial-state protocol. Moreover, among constant-state protocols, this protocol has near-optimal average case complexity on dense random graphs.","lang":"eng"}],"title":"Near-optimal leader election in population protocols on graphs","status":"public","file":[{"success":1,"checksum":"4c6b29172b8e355b4fbc364a2e0827b2","access_level":"open_access","file_id":"11854","file_size":1593474,"content_type":"application/pdf","date_updated":"2022-08-16T08:05:15Z","date_created":"2022-08-16T08:05:15Z","creator":"cchlebak","file_name":"2022_PODC_Alistarh.pdf","relation":"main_file"}],"year":"2022","ec_funded":1,"file_date_updated":"2022-08-16T08:05:15Z","has_accepted_license":"1","conference":{"location":"Salerno, Italy","start_date":"2022-07-25","end_date":"2022-07-29","name":"PODC: Symposium on Principles of Distributed Computing"},"publisher":"Association for Computing Machinery","publication_status":"published","publication_identifier":{"isbn":["9781450392624"]},"arxiv":1,"language":[{"iso":"eng"}],"scopus_import":"1","day":"21","project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"citation":{"apa":"Alistarh, D.-A., Rybicki, J., &#38; Voitovych, S. (2022). Near-optimal leader election in population protocols on graphs. In <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i> (pp. 246–256). Salerno, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519270.3538435\">https://doi.org/10.1145/3519270.3538435</a>","short":"D.-A. Alistarh, J. Rybicki, S. Voitovych, in:, Proceedings of the Annual ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2022, pp. 246–256.","ama":"Alistarh D-A, Rybicki J, Voitovych S. Near-optimal leader election in population protocols on graphs. In: <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2022:246-256. doi:<a href=\"https://doi.org/10.1145/3519270.3538435\">10.1145/3519270.3538435</a>","chicago":"Alistarh, Dan-Adrian, Joel Rybicki, and Sasha Voitovych. “Near-Optimal Leader Election in Population Protocols on Graphs.” In <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>, 246–56. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519270.3538435\">https://doi.org/10.1145/3519270.3538435</a>.","ista":"Alistarh D-A, Rybicki J, Voitovych S. 2022. Near-optimal leader election in population protocols on graphs. Proceedings of the Annual ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 246–256.","ieee":"D.-A. Alistarh, J. Rybicki, and S. Voitovych, “Near-optimal leader election in population protocols on graphs,” in <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>, Salerno, Italy, 2022, pp. 246–256.","mla":"Alistarh, Dan-Adrian, et al. “Near-Optimal Leader Election in Population Protocols on Graphs.” <i>Proceedings of the Annual ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2022, pp. 246–56, doi:<a href=\"https://doi.org/10.1145/3519270.3538435\">10.1145/3519270.3538435</a>."},"publication":"Proceedings of the Annual ACM Symposium on Principles of Distributed Computing","date_created":"2022-08-14T22:01:46Z","acknowledgement":"We thank the anonymous reviewers for their helpful comments. We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki","first_name":"Joel"},{"full_name":"Voitovych, Sasha","last_name":"Voitovych","first_name":"Sasha"}],"doi":"10.1145/3519270.3538435","month":"07","corr_author":"1","ddc":["000"],"oa":1,"external_id":{"isi":["001031439100030"],"arxiv":["2205.12597"]},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-12-30T09:04:17Z","date_published":"2022-07-21T00:00:00Z"},{"date_updated":"2024-10-09T21:03:06Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_published":"2022-06-01T00:00:00Z","external_id":{"isi":["000809108500001"]},"article_number":"56","doi":"10.1007/s00028-022-00786-7","article_type":"original","oa":1,"ddc":["510"],"corr_author":"1","month":"06","author":[{"first_name":"Antonio","last_name":"Agresti","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"date_created":"2022-08-16T08:39:43Z","publication":"Journal of Evolution Equations","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"The authors thank Emiel Lorist for helpful comments. The authors thank the anonymous referees for their helpful remarks to improve the presentation.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","citation":{"apa":"Agresti, A., &#38; Veraar, M. (2022). Nonlinear parabolic stochastic evolution equations in critical spaces part II. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00786-7\">https://doi.org/10.1007/s00028-022-00786-7</a>","ieee":"A. Agresti and M. Veraar, “Nonlinear parabolic stochastic evolution equations in critical spaces part II,” <i>Journal of Evolution Equations</i>, vol. 22, no. 2. Springer Nature, 2022.","ama":"Agresti A, Veraar M. Nonlinear parabolic stochastic evolution equations in critical spaces part II. <i>Journal of Evolution Equations</i>. 2022;22(2). doi:<a href=\"https://doi.org/10.1007/s00028-022-00786-7\">10.1007/s00028-022-00786-7</a>","short":"A. Agresti, M. Veraar, Journal of Evolution Equations 22 (2022).","chicago":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part II.” <i>Journal of Evolution Equations</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00028-022-00786-7\">https://doi.org/10.1007/s00028-022-00786-7</a>.","ista":"Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations in critical spaces part II. Journal of Evolution Equations. 22(2), 56.","mla":"Agresti, Antonio, and Mark Veraar. “Nonlinear Parabolic Stochastic Evolution Equations in Critical Spaces Part II.” <i>Journal of Evolution Equations</i>, vol. 22, no. 2, 56, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s00028-022-00786-7\">10.1007/s00028-022-00786-7</a>."},"publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"day":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publisher":"Springer Nature","issue":"2","has_accepted_license":"1","volume":22,"file_date_updated":"2022-08-16T08:52:46Z","year":"2022","file":[{"content_type":"application/pdf","creator":"kschuh","date_updated":"2022-08-16T08:52:46Z","date_created":"2022-08-16T08:52:46Z","relation":"main_file","file_name":"2022_Journal of Evolution Equations_Agresti.pdf","success":1,"checksum":"59b99d1b48b6bd40983e7ce298524a21","access_level":"open_access","file_id":"11862","file_size":1758371}],"intvolume":"        22","status":"public","type":"journal_article","title":"Nonlinear parabolic stochastic evolution equations in critical spaces part II","abstract":[{"text":"This paper is a continuation of Part I of this project, where we developed a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian noise. In the current Part II we consider blow-up criteria and regularization phenomena. As in Part I we can allow nonlinearities with polynomial growth and rough initial values from critical spaces. In the first main result we obtain several new blow-up criteria for quasi- and semilinear stochastic evolution equations. In particular, for semilinear equations we obtain a Serrin type blow-up criterium, which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074, 2018) to the stochastic setting. Blow-up criteria can be used to prove global well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights in time play a central role in the proofs. Our second contribution is a new method to bootstrap Sobolev and Hölder regularity in time and space, which does not require smoothness of the initial data. The blow-up criteria are at the basis of these new methods. Moreover, in applications the bootstrap results can be combined with our blow-up criteria, to obtain efficient ways to prove global existence. This gives new results even in classical 𝐿2-settings, which we illustrate for a concrete SPDE. In future works in preparation we apply the results of the current paper to obtain global well-posedness results and regularity for several concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into a more flexible framework, where less restrictions on the nonlinearities are needed, and we are able to treat rough initial values from critical spaces. Moreover, we will obtain higher-order regularity results.","lang":"eng"}],"department":[{"_id":"JuFi"}],"isi":1,"keyword":["Mathematics (miscellaneous)"],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","_id":"11858"},{"corr_author":"1","month":"07","oa":1,"ddc":["510"],"article_type":"original","doi":"10.1007/s43036-022-00199-w","author":[{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior"}],"date_published":"2022-07-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","date_updated":"2024-10-09T21:03:07Z","article_number":"38","language":[{"iso":"eng"}],"scopus_import":"1","day":"01","publication_identifier":{"eissn":["2538-225X"]},"publisher":"Springer Nature","publication_status":"published","acknowledgement":"The author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2. The author would like to thank Daniel Lenz for his support and encouragement during the author’s ongoing graduate studies and him as well as Marcel Schmidt for fruitful discussions on domination of quadratic forms. He wants to thank Batu Güneysu and Peter Stollmann for valuable comments on a preliminary version of this article. He would also like to thank the organizers of the conference Analysis and Geometry on Graphs and Manifolds in Potsdam, where the initial motivation of this article was conceived, and the organizers of the intense activity period Metric Measure Spaces and Ricci Curvature at MPIM in Bonn, where this work was finished.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Advances in Operator Theory","date_created":"2022-08-18T07:22:24Z","citation":{"ieee":"M. Wirth, “Kac regularity and domination of quadratic forms,” <i>Advances in Operator Theory</i>, vol. 7, no. 3. Springer Nature, 2022.","ama":"Wirth M. Kac regularity and domination of quadratic forms. <i>Advances in Operator Theory</i>. 2022;7(3). doi:<a href=\"https://doi.org/10.1007/s43036-022-00199-w\">10.1007/s43036-022-00199-w</a>","short":"M. Wirth, Advances in Operator Theory 7 (2022).","chicago":"Wirth, Melchior. “Kac Regularity and Domination of Quadratic Forms.” <i>Advances in Operator Theory</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s43036-022-00199-w\">https://doi.org/10.1007/s43036-022-00199-w</a>.","ista":"Wirth M. 2022. Kac regularity and domination of quadratic forms. Advances in Operator Theory. 7(3), 38.","apa":"Wirth, M. (2022). Kac regularity and domination of quadratic forms. <i>Advances in Operator Theory</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s43036-022-00199-w\">https://doi.org/10.1007/s43036-022-00199-w</a>","mla":"Wirth, Melchior. “Kac Regularity and Domination of Quadratic Forms.” <i>Advances in Operator Theory</i>, vol. 7, no. 3, 38, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s43036-022-00199-w\">10.1007/s43036-022-00199-w</a>."},"year":"2022","intvolume":"         7","status":"public","file":[{"file_name":"2022_AdvancesOperatorTheory_Wirth.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2022-08-18T08:02:34Z","date_updated":"2022-08-18T08:02:34Z","creator":"dernst","file_size":389060,"file_id":"11921","access_level":"open_access","checksum":"913474844a1b38264fb710746d5e2e98","success":1}],"volume":7,"has_accepted_license":"1","issue":"3","file_date_updated":"2022-08-18T08:02:34Z","article_processing_charge":"Yes (via OA deal)","_id":"11916","quality_controlled":"1","abstract":[{"lang":"eng","text":"A domain is called Kac regular for a quadratic form on L2 if every functions vanishing almost everywhere outside the domain can be approximated in form norm by functions with compact support in the domain. It is shown that this notion is stable under domination of quadratic forms. As applications measure perturbations of quasi-regular Dirichlet forms, Cheeger energies on metric measure spaces and Schrödinger operators on manifolds are studied. Along the way a characterization of the Sobolev space with Dirichlet boundary conditions on domains in infinitesimally Riemannian metric measure spaces is obtained."}],"title":"Kac regularity and domination of quadratic forms","type":"journal_article","keyword":["Algebra and Number Theory","Analysis"],"department":[{"_id":"JaMa"}]},{"ec_funded":1,"year":"2022","intvolume":"       188","status":"public","file":[{"creator":"dernst","date_updated":"2022-08-18T08:09:00Z","date_created":"2022-08-18T08:09:00Z","content_type":"application/pdf","file_name":"2022_JournalStatisticalPhysics_Rademacher.pdf","relation":"main_file","file_id":"11922","file_size":483481,"success":1,"checksum":"44418cb44f07fa21ed3907f85abf7f39","access_level":"open_access"}],"has_accepted_license":"1","volume":188,"file_date_updated":"2022-08-18T08:09:00Z","article_processing_charge":"Yes (via OA deal)","_id":"11917","quality_controlled":"1","abstract":[{"text":"We study the many-body dynamics of an initially factorized bosonic wave function in the mean-field regime. We prove large deviation estimates for the fluctuations around the condensate. We derive an upper bound extending a recent result to more general interactions. Furthermore, we derive a new lower bound which agrees with the upper bound in leading order.","lang":"eng"}],"title":"Large deviation estimates for weakly interacting bosons","type":"journal_article","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"isi":1,"department":[{"_id":"RoSe"}],"corr_author":"1","month":"07","oa":1,"ddc":["510"],"article_type":"original","doi":"10.1007/s10955-022-02940-4","author":[{"orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"date_published":"2022-07-01T00:00:00Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-04-14T07:26:59Z","article_number":"9","external_id":{"isi":["000805175000001"]},"scopus_import":"1","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"day":"01","publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]},"publication_status":"published","publisher":"Springer Nature","acknowledgement":"The authors thank Gérard Ben Arous for pointing out the question of a lower bound. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC Grant Agreement No. 694227 (R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged.\r\nOpen access funding provided by IST Austria.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Journal of Statistical Physics","date_created":"2022-08-18T07:23:26Z","citation":{"mla":"Rademacher, Simone Anna Elvira, and Robert Seiringer. “Large Deviation Estimates for Weakly Interacting Bosons.” <i>Journal of Statistical Physics</i>, vol. 188, 9, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s10955-022-02940-4\">10.1007/s10955-022-02940-4</a>.","apa":"Rademacher, S. A. E., &#38; Seiringer, R. (2022). Large deviation estimates for weakly interacting bosons. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-022-02940-4\">https://doi.org/10.1007/s10955-022-02940-4</a>","ieee":"S. A. E. Rademacher and R. Seiringer, “Large deviation estimates for weakly interacting bosons,” <i>Journal of Statistical Physics</i>, vol. 188. Springer Nature, 2022.","ama":"Rademacher SAE, Seiringer R. Large deviation estimates for weakly interacting bosons. <i>Journal of Statistical Physics</i>. 2022;188. doi:<a href=\"https://doi.org/10.1007/s10955-022-02940-4\">10.1007/s10955-022-02940-4</a>","short":"S.A.E. Rademacher, R. Seiringer, Journal of Statistical Physics 188 (2022).","chicago":"Rademacher, Simone Anna Elvira, and Robert Seiringer. “Large Deviation Estimates for Weakly Interacting Bosons.” <i>Journal of Statistical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10955-022-02940-4\">https://doi.org/10.1007/s10955-022-02940-4</a>.","ista":"Rademacher SAE, Seiringer R. 2022. Large deviation estimates for weakly interacting bosons. Journal of Statistical Physics. 188, 9."}},{"has_accepted_license":"1","volume":13,"pmid":1,"file_date_updated":"2022-08-22T06:33:02Z","year":"2022","status":"public","intvolume":"        13","file":[{"content_type":"application/pdf","date_created":"2022-08-22T06:33:02Z","creator":"dernst","date_updated":"2022-08-22T06:33:02Z","file_name":"2022_NatureCommunications_Reinhardt.pdf","relation":"main_file","file_id":"11939","file_size":1767206,"success":1,"checksum":"8ff9b689cde59fd3a9959a9f01929dea","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII′ and X are the same thermodynamic phase under different conditions, whereas superionic ice VII″ has a first-order phase boundary with ice VII′. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems."}],"title":"Thermodynamics of high-pressure ice phases explored with atomistic simulations","type":"journal_article","isi":1,"department":[{"_id":"BiCh"}],"article_processing_charge":"No","_id":"11937","quality_controlled":"1","date_published":"2022-08-10T00:00:00Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-10-09T21:03:16Z","article_number":"4707","external_id":{"isi":["000838655300022"],"pmid":["35948550"]},"month":"08","corr_author":"1","oa":1,"ddc":["540"],"article_type":"original","doi":"10.1038/s41467-022-32374-1","author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"first_name":"Mandy","full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen"},{"full_name":"Coppari, Federica","last_name":"Coppari","first_name":"Federica"},{"full_name":"Millot, Marius","last_name":"Millot","first_name":"Marius"},{"last_name":"Hamel","full_name":"Hamel, Sebastien","first_name":"Sebastien"},{"last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"acknowledgement":"We thank Chris Pickard for providing the initial structures of high-pressure ice phases and for useful advice. A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. M.B. was supported by the European Union within the Marie Skłodowska-Curie actions (xICE grant 894725) and acknowledges computational resources at North-German Supercomputing Alliance (HLRN) facilities. S.H. and M.M. acknowledge support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge programme. F.C. acknowledges support from the US DOE Office of Science, Office of Fusion Energy Sciences. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature Communications","date_created":"2022-08-21T22:01:55Z","citation":{"ama":"Reinhardt A, Bethkenhagen M, Coppari F, Millot M, Hamel S, Cheng B. Thermodynamics of high-pressure ice phases explored with atomistic simulations. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32374-1\">10.1038/s41467-022-32374-1</a>","short":"A. Reinhardt, M. Bethkenhagen, F. Coppari, M. Millot, S. Hamel, B. Cheng, Nature Communications 13 (2022).","ista":"Reinhardt A, Bethkenhagen M, Coppari F, Millot M, Hamel S, Cheng B. 2022. Thermodynamics of high-pressure ice phases explored with atomistic simulations. Nature Communications. 13, 4707.","chicago":"Reinhardt, Aleks, Mandy Bethkenhagen, Federica Coppari, Marius Millot, Sebastien Hamel, and Bingqing Cheng. “Thermodynamics of High-Pressure Ice Phases Explored with Atomistic Simulations.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32374-1\">https://doi.org/10.1038/s41467-022-32374-1</a>.","ieee":"A. Reinhardt, M. Bethkenhagen, F. Coppari, M. Millot, S. Hamel, and B. Cheng, “Thermodynamics of high-pressure ice phases explored with atomistic simulations,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","apa":"Reinhardt, A., Bethkenhagen, M., Coppari, F., Millot, M., Hamel, S., &#38; Cheng, B. (2022). Thermodynamics of high-pressure ice phases explored with atomistic simulations. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32374-1\">https://doi.org/10.1038/s41467-022-32374-1</a>","mla":"Reinhardt, Aleks, et al. “Thermodynamics of High-Pressure Ice Phases Explored with Atomistic Simulations.” <i>Nature Communications</i>, vol. 13, 4707, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32374-1\">10.1038/s41467-022-32374-1</a>."},"scopus_import":"1","language":[{"iso":"eng"}],"day":"10","publication_identifier":{"eissn":["2041-1723"]},"publisher":"Springer Nature","publication_status":"published"}]