[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11707","ec_funded":1,"publication_identifier":{"isbn":["9783031099922"],"eissn":["1611-3349"],"issn":["0302-9743"]},"citation":{"ieee":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, and J. Suomela, “Local mending,” in <i>International Colloquium on Structural Information and Communication Complexity</i>, Paderborn, Germany, 2022, vol. 13298, pp. 1–20.","chicago":"Balliu, Alkida, Juho Hirvonen, Darya Melnyk, Dennis Olivetti, Joel Rybicki, and Jukka Suomela. “Local Mending.” In <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, 13298:1–20. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>.","mla":"Balliu, Alkida, et al. “Local Mending.” <i>International Colloquium on Structural Information and Communication Complexity</i>, edited by Merav Parter, vol. 13298, Springer Nature, 2022, pp. 1–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>.","short":"A. Balliu, J. Hirvonen, D. Melnyk, D. Olivetti, J. Rybicki, J. Suomela, in:, M. Parter (Ed.), International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2022, pp. 1–20.","ista":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. 2022. Local mending. International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication ComplexityLNCS vol. 13298, 1–20.","apa":"Balliu, A., Hirvonen, J., Melnyk, D., Olivetti, D., Rybicki, J., &#38; Suomela, J. (2022). Local mending. In M. Parter (Ed.), <i>International Colloquium on Structural Information and Communication Complexity</i> (Vol. 13298, pp. 1–20). Paderborn, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">https://doi.org/10.1007/978-3-031-09993-9_1</a>","ama":"Balliu A, Hirvonen J, Melnyk D, Olivetti D, Rybicki J, Suomela J. Local mending. In: Parter M, ed. <i>International Colloquium on Structural Information and Communication Complexity</i>. Vol 13298. LNCS. Springer Nature; 2022:1-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-09993-9_1\">10.1007/978-3-031-09993-9_1</a>"},"editor":[{"first_name":"Merav","last_name":"Parter","full_name":"Parter, Merav"}],"quality_controlled":"1","department":[{"_id":"DaAl"}],"title":"Local mending","main_file_link":[{"url":"https://arxiv.org/abs/2102.08703","open_access":"1"}],"date_created":"2022-07-31T22:01:49Z","month":"06","oa":1,"scopus_import":"1","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605. This work was supported in part by the Academy of Finland, Grants 314888 and 333837. The authors would also like to thank David Harris, Neven Villani, and the anonymous reviewers for their very helpful comments and feedback on previous versions of this work.","publication_status":"published","year":"2022","arxiv":1,"external_id":{"isi":["000876977400001"],"arxiv":["2102.08703"]},"intvolume":"     13298","date_updated":"2025-04-14T07:50:55Z","day":"25","project":[{"name":"Coordination in constrained and natural distributed systems","grant_number":"840605","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"isi":1,"publisher":"Springer Nature","author":[{"first_name":"Alkida","full_name":"Balliu, Alkida","last_name":"Balliu"},{"first_name":"Juho","last_name":"Hirvonen","full_name":"Hirvonen, Juho"},{"full_name":"Melnyk, Darya","last_name":"Melnyk","first_name":"Darya"},{"first_name":"Dennis","full_name":"Olivetti, Dennis","last_name":"Olivetti"},{"full_name":"Rybicki, Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"type":"conference","oa_version":"Preprint","conference":{"name":"SIROCCO: Structural Information and Communication Complexity","start_date":"2022-06-27","location":"Paderborn, Germany","end_date":"2022-06-29"},"publication":"International Colloquium on Structural Information and Communication Complexity","status":"public","abstract":[{"text":"In this work we introduce the graph-theoretic notion of mendability: for each locally checkable graph problem we can define its mending radius, which captures the idea of how far one needs to modify a partial solution in order to “patch a hole.” We explore how mendability is connected to the existence of efficient algorithms, especially in distributed, parallel, and fault-tolerant settings. It is easy to see that O(1)-mendable problems are also solvable in O(log∗n) rounds in the LOCAL model of distributed computing. One of the surprises is that in paths and cycles, a converse also holds in the following sense: if a problem Π can be solved in O(log∗n), there is always a restriction Π′⊆Π that is still efficiently solvable but that is also O(1)-mendable. We also explore the structure of the landscape of mendability. For example, we show that in trees, the mending radius of any locally checkable problem is O(1), Θ(logn), or Θ(n), while in general graphs the structure is much more diverse.","lang":"eng"}],"series_title":"LNCS","date_published":"2022-06-25T00:00:00Z","language":[{"iso":"eng"}],"volume":13298,"doi":"10.1007/978-3-031-09993-9_1","article_processing_charge":"No","page":"1-20"},{"article_processing_charge":"No","doi":"10.5281/ZENODO.6802720","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11704"}]},"year":"2022","date_published":"2022-07-06T00:00:00Z","ddc":["000"],"status":"public","abstract":[{"lang":"eng","text":"Codes and data for reproducing the results of N. B. Budanur and B. Hof \"An autonomous compartmental model for accelerating epidemics\""}],"corr_author":"1","oa":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"07","oa_version":"Published Version","type":"research_data_reference","date_created":"2022-08-01T08:06:33Z","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.6802720","open_access":"1"}],"department":[{"_id":"BjHo"}],"title":"burakbudanur/autoacc-public","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"publisher":"Zenodo","has_accepted_license":"1","author":[{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B"}],"citation":{"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>.","ieee":"N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022.","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>.","ista":"Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>.","short":"N.B. Budanur, (2022).","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>","ama":"Budanur NB. burakbudanur/autoacc-public. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6802720\">10.5281/ZENODO.6802720</a>"},"day":"06","_id":"11711","date_updated":"2025-06-11T13:37:36Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"citation":{"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>","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>","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).","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>.","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>.","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."},"has_accepted_license":"1","date_created":"2022-08-01T09:04:27Z","title":"Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli","quality_controlled":"1","department":[{"_id":"CaGu"}],"_id":"11713","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1756-0500"]},"article_number":"173","external_id":{"pmid":["35562780"]},"year":"2022","intvolume":"        15","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13104-022-06152-7"}]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Medicine"],"month":"05","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.","ddc":["570"],"publication_status":"published","article_type":"letter_note","oa":1,"scopus_import":"1","publisher":"Springer Nature","author":[{"last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"first_name":"Martina","full_name":"Sauert, Martina","last_name":"Sauert"},{"full_name":"Albanese, Tanino G.","last_name":"Albanese","first_name":"Tanino G."},{"full_name":"Moll, Isabella","last_name":"Moll","first_name":"Isabella"}],"type":"journal_article","date_updated":"2025-04-14T09:24:53Z","project":[{"name":"Bacterial toxin-antitoxin systems as antiphage defense mechanisms","grant_number":"V00738","call_identifier":"FWF","_id":"26956E74-B435-11E9-9278-68D0E5697425"}],"day":"13","language":[{"iso":"eng"}],"date_published":"2022-05-13T00:00:00Z","file_date_updated":"2022-08-01T09:24:42Z","doi":"10.1186/s13104-022-06061-9","article_processing_charge":"No","volume":15,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"corr_author":"1","status":"public","file":[{"checksum":"008156e5340e9789f0f6d82bde4d347a","date_created":"2022-08-01T09:24:42Z","relation":"main_file","success":1,"content_type":"application/pdf","file_size":1545310,"creator":"dernst","access_level":"open_access","file_name":"2022_BMCResearchNotes_Nikolic.pdf","file_id":"11714","date_updated":"2022-08-01T09:24:42Z"}],"publication":"BMC Research Notes"},{"date_created":"2022-08-01T17:08:16Z","department":[{"_id":"VaKa"}],"quality_controlled":"1","title":"Rigidity of Newton dynamics","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","citation":{"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>.","ieee":"K. Drach and D. Schleicher, “Rigidity of Newton dynamics,” <i>Advances in Mathematics</i>, vol. 408, no. Part A. Elsevier, 2022.","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>.","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>","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>"},"publication_identifier":{"issn":["0001-8708"]},"ec_funded":1,"article_number":"108591","_id":"11717","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       408","keyword":["General Mathematics"],"year":"2022","external_id":{"isi":["000860924200005"]},"publication_status":"published","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).","ddc":["510"],"scopus_import":"1","oa":1,"article_type":"original","month":"10","type":"journal_article","publisher":"Elsevier","author":[{"full_name":"Drach, Kostiantyn","last_name":"Drach","id":"fe8209e2-906f-11eb-847d-950f8fc09115","first_name":"Kostiantyn","orcid":"0000-0002-9156-8616"},{"full_name":"Schleicher, Dierk","last_name":"Schleicher","first_name":"Dierk"}],"isi":1,"project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows"}],"day":"29","date_updated":"2025-04-14T07:53:45Z","doi":"10.1016/j.aim.2022.108591","article_processing_charge":"Yes (via OA deal)","volume":408,"file_date_updated":"2023-02-02T07:39:09Z","language":[{"iso":"eng"}],"date_published":"2022-10-29T00:00:00Z","status":"public","abstract":[{"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.","lang":"eng"}],"corr_author":"1","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-02-02T07:39:09Z","file_id":"12474","file_name":"2022_AdvancesMathematics_Drach.pdf","creator":"dernst","file_size":2164036,"date_created":"2023-02-02T07:39:09Z","checksum":"2710e6f5820f8c20a676ddcbb30f0e8d","relation":"main_file","success":1}],"publication":"Advances in Mathematics","issue":"Part A","oa_version":"Published Version"},{"author":[{"orcid":"0000-0002-5607-272X","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Lanxin"},{"first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen"},{"last_name":"Alotaibi","full_name":"Alotaibi, Saqer S.","first_name":"Saqer S."},{"first_name":"Aleš","full_name":"Pěnčík, Aleš","last_name":"Pěnčík"},{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"publisher":"National Academy of Sciences","type":"journal_article","date_updated":"2025-05-14T11:01:00Z","day":"25","project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"isi":1,"file_date_updated":"2022-08-08T07:42:09Z","language":[{"iso":"eng"}],"date_published":"2022-07-25T00:00:00Z","volume":119,"doi":"10.1073/pnas.2121058119","article_processing_charge":"No","oa_version":"Published Version","file":[{"success":1,"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","date_created":"2022-08-08T07:42:09Z","relation":"main_file","creator":"dernst","file_size":2506262,"access_level":"open_access","file_id":"11747","date_updated":"2022-08-08T07:42:09Z","file_name":"2022_PNAS_Li.pdf","content_type":"application/pdf"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"31","status":"public","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"}],"corr_author":"1","has_accepted_license":"1","citation":{"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>","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>","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.","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).","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>.","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."},"pmid":1,"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)"},"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","date_created":"2022-08-04T20:06:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11723","article_number":"e2121058119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2022","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"keyword":["Multidisciplinary"],"intvolume":"       119","month":"07","oa":1,"article_type":"original","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","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","ddc":["580"]},{"publication_identifier":{"eissn":["1091-6490"]},"article_number":"e2121279119","_id":"11733","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-08-07T22:01:56Z","department":[{"_id":"MaRo"}],"quality_controlled":"1","title":"Improving GWAS discovery and genomic prediction accuracy in biobank data","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)"},"has_accepted_license":"1","pmid":1,"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>.","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>.","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.","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>","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>","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.","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)."},"publication_status":"published","ddc":["570"],"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.","oa":1,"article_type":"original","scopus_import":"1","month":"07","intvolume":"       119","related_material":{"record":[{"relation":"research_data","status":"public","id":"13064"}]},"year":"2022","external_id":{"pmid":["35905320"],"isi":["000881496900003"]},"isi":1,"day":"29","date_updated":"2025-06-12T06:22:37Z","type":"journal_article","author":[{"last_name":"Orliac","full_name":"Orliac, Etienne J.","first_name":"Etienne J."},{"full_name":"Trejo Banos, Daniel","last_name":"Trejo Banos","first_name":"Daniel"},{"first_name":"Sven E.","last_name":"Ojavee","full_name":"Ojavee, Sven E."},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"full_name":"Mägi, Reedik","last_name":"Mägi","first_name":"Reedik"},{"last_name":"Visscher","full_name":"Visscher, Peter M.","first_name":"Peter M."},{"orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson"}],"publisher":"National Academy of Sciences","status":"public","abstract":[{"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.","lang":"eng"}],"corr_author":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"success":1,"relation":"main_file","date_created":"2022-08-08T07:31:19Z","checksum":"b5d2024e19fbad6f85a5e384e44d0f3b","file_name":"2022_PNAS_Orliac.pdf","date_updated":"2022-08-08T07:31:19Z","file_id":"11745","access_level":"open_access","creator":"dernst","file_size":1001164,"content_type":"application/pdf"}],"issue":"31","oa_version":"Published Version","doi":"10.1073/pnas.2121279119","article_processing_charge":"No","volume":119,"file_date_updated":"2022-08-08T07:31:19Z","date_published":"2022-07-29T00:00:00Z","language":[{"iso":"eng"}]},{"type":"journal_article","publisher":"National Academy of Sciences","author":[{"first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415","last_name":"Abualia","full_name":"Abualia, Rashed"},{"full_name":"Ötvös, Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","first_name":"Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"first_name":"Eleonore","last_name":"Bouguyon","full_name":"Bouguyon, Eleonore"},{"orcid":"0000-0002-1215-4264","first_name":"Kevin","id":"a24c7829-16e8-11ed-8527-c4d36ffb7539","last_name":"Domanegg","full_name":"Domanegg, Kevin"},{"first_name":"Anne","last_name":"Krapp","full_name":"Krapp, Anne"},{"full_name":"Nacry, Philip","last_name":"Nacry","first_name":"Philip"},{"last_name":"Gojon","full_name":"Gojon, Alain","first_name":"Alain"},{"full_name":"Lacombe, Benoit","last_name":"Lacombe","first_name":"Benoit"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"}],"day":"25","isi":1,"project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-05-14T11:00:29Z","volume":119,"article_processing_charge":"No","doi":"10.1073/pnas.2122460119","file_date_updated":"2022-08-08T07:09:58Z","date_published":"2022-07-25T00:00:00Z","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_updated":"2022-08-08T07:09:58Z","file_name":"2022_PNAS_Abualia.pdf","file_id":"11744","access_level":"open_access","file_size":3092330,"creator":"dernst","relation":"main_file","date_created":"2022-08-08T07:09:58Z","checksum":"6e97dedc281247fc3fe238a209f14af0","success":1}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"31","status":"public","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"}],"corr_author":"1","oa_version":"Published Version","department":[{"_id":"EvBe"}],"quality_controlled":"1","title":"Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses","date_created":"2022-08-07T22:01:57Z","has_accepted_license":"1","citation":{"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>.","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.","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>","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>","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)."},"pmid":1,"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)"},"article_number":"e2122460119","publication_identifier":{"eissn":["1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11734","intvolume":"       119","year":"2022","external_id":{"isi":["000881496900007"],"pmid":["35878040"]},"article_type":"original","oa":1,"scopus_import":"1","ddc":["570"],"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).","publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"07"},{"month":"07","oa":1,"article_type":"original","scopus_import":"1","ddc":["000"],"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).","publication_status":"published","external_id":{"isi":["000830989200018"]},"year":"2022","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/unlocking-interlocking-riddles/"}]},"intvolume":"        41","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11735","ec_funded":1,"article_number":"150","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"citation":{"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>.","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>.","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.","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>","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>","ista":"Chen R, Wang Z, Song P, Bickel B. 2022. Computational design of high-level interlocking puzzles. ACM Transactions on Graphics. 41(4), 150.","short":"R. Chen, Z. Wang, P. Song, B. Bickel, ACM Transactions on Graphics 41 (2022)."},"has_accepted_license":"1","title":"Computational design of high-level interlocking puzzles","department":[{"_id":"BeBi"}],"quality_controlled":"1","date_created":"2022-08-07T22:01:57Z","oa_version":"Submitted Version","issue":"4","file":[{"success":1,"relation":"main_file","date_created":"2022-08-28T07:56:19Z","checksum":"0b51651be45b1b33f2072bd5d2686c69","creator":"bbickel","file_size":16896871,"file_id":"11992","file_name":"Chen-2022-High-LevelPuzzle_authorVersion.pdf","date_updated":"2022-08-28T07:56:19Z","access_level":"open_access","content_type":"application/pdf"}],"publication":"ACM Transactions on Graphics","abstract":[{"lang":"eng","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."}],"status":"public","date_published":"2022-07-22T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2022-08-28T07:56:19Z","volume":41,"article_processing_charge":"No","doi":"10.1145/3528223.3530071","date_updated":"2025-04-14T07:28:57Z","day":"22","isi":1,"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"author":[{"full_name":"Chen, Rulin","last_name":"Chen","first_name":"Rulin"},{"first_name":"Ziqi","full_name":"Wang, Ziqi","last_name":"Wang"},{"last_name":"Song","full_name":"Song, Peng","first_name":"Peng"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"}],"publisher":"Association for Computing Machinery","type":"journal_article"},{"date_updated":"2026-06-18T17:20:41Z","isi":1,"day":"22","publisher":"Association for Computing Machinery","author":[{"first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg","last_name":"Sperl"},{"last_name":"Sánchez-Banderas","full_name":"Sánchez-Banderas, Rosa M.","first_name":"Rosa M."},{"first_name":"Manwen","last_name":"Li","full_name":"Li, Manwen"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"first_name":"Miguel A.","last_name":"Otaduy","full_name":"Otaduy, Miguel A."}],"type":"journal_article","oa_version":"Published Version","status":"public","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"}],"publication":"ACM Transactions on Graphics","issue":"4","language":[{"iso":"eng"}],"date_published":"2022-07-22T00:00:00Z","article_processing_charge":"No","doi":"10.1145/3528223.3530167","volume":41,"_id":"11736","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"article_number":"65","citation":{"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>","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>","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.","short":"G. Sperl, R.M. Sánchez-Banderas, M. Li, C. Wojtan, M.A. Otaduy, ACM Transactions on Graphics 41 (2022).","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>.","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>.","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."},"date_created":"2022-08-07T22:01:58Z","main_file_link":[{"url":"https://doi.org/10.1145/3528223.3530167","open_access":"1"}],"department":[{"_id":"ChWo"}],"quality_controlled":"1","title":"Estimation of yarn-level simulation models for production fabrics","month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"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","ddc":["000"],"scopus_import":"1","article_type":"original","oa":1,"year":"2022","external_id":{"isi":["000830989200114"]},"intvolume":"        41","related_material":{"record":[{"id":"12358","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/digital-yarn-real-socks/","description":"News on the ISTA website","relation":"press_release"}]}},{"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"article_number":"045302","_id":"11737","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-08-07T22:01:58Z","title":"Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells","quality_controlled":"1","department":[{"_id":"ZhAl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"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>","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>","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).","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.","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>."},"has_accepted_license":"1","publication_status":"published","acknowledgement":"This work was supported by the Austrian Science Funds (W 1243, I 3456-N27, I 5539-N).","ddc":["530"],"oa":1,"scopus_import":"1","article_type":"original","month":"07","intvolume":"       106","external_id":{"isi":["000834349200010"]},"year":"2022","isi":1,"day":"15","date_updated":"2023-08-03T12:38:57Z","type":"journal_article","publisher":"American Physical Society","author":[{"orcid":"0000-0002-1648-0999","first_name":"Uladzislau","id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","last_name":"Dziom","full_name":"Dziom, Uladzislau"},{"first_name":"A.","full_name":"Shuvaev, A.","last_name":"Shuvaev"},{"first_name":"J.","last_name":"Gospodarič","full_name":"Gospodarič, J."},{"first_name":"E. G.","full_name":"Novik, E. G.","last_name":"Novik"},{"last_name":"Dobretsova","full_name":"Dobretsova, A. A.","first_name":"A. A."},{"first_name":"N. N.","full_name":"Mikhailov, N. N.","last_name":"Mikhailov"},{"first_name":"Z. D.","full_name":"Kvon, Z. D.","last_name":"Kvon"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"},{"first_name":"A.","full_name":"Pimenov, A.","last_name":"Pimenov"}],"abstract":[{"lang":"eng","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."}],"status":"public","issue":"4","publication":"Physical Review B","file":[{"date_created":"2022-08-08T06:58:22Z","checksum":"115aff9e0cde2f806cb26953d7262791","relation":"main_file","success":1,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_PhysRevB_Dziom.pdf","file_id":"11743","date_updated":"2022-08-08T06:58:22Z","file_size":774455,"creator":"dernst"}],"oa_version":"Published Version","doi":"10.1103/PhysRevB.106.045302","article_processing_charge":"No","volume":106,"date_published":"2022-07-15T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2022-08-08T06:58:22Z"},{"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"ec_funded":1,"_id":"11739","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2008.10962"}],"date_created":"2022-08-07T22:01:59Z","quality_controlled":"1","department":[{"_id":"JaMa"}],"title":"Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","citation":{"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>.","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.","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>.","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>","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>","short":"D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis 54 (2022) 4297–4333.","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."},"publication_status":"published","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.","article_type":"original","oa":1,"scopus_import":"1","month":"07","intvolume":"        54","keyword":["Fokker--Planck equation","gradient flow","evolutionary $\\Gamma$-convergence"],"related_material":{"record":[{"id":"10022","status":"public","relation":"earlier_version"}]},"year":"2022","external_id":{"isi":["000889274600001"],"arxiv":["2008.10962"]},"arxiv":1,"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and dispersion in nonlinear partial differential equations","grant_number":"W1245"}],"isi":1,"day":"18","date_updated":"2025-04-15T08:31:31Z","type":"journal_article","author":[{"first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","full_name":"Forkert, Dominik L"},{"full_name":"Maas, Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"publisher":"Society for Industrial and Applied Mathematics","status":"public","corr_author":"1","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."}],"publication":"SIAM Journal on Mathematical Analysis","issue":"4","oa_version":"Preprint","article_processing_charge":"No","doi":"10.1137/21M1410968","page":"4297-4333","volume":54,"language":[{"iso":"eng"}],"date_published":"2022-07-18T00:00:00Z"},{"isi":1,"day":"29","date_updated":"2024-10-09T21:03:03Z","type":"journal_article","author":[{"last_name":"Cooley","full_name":"Cooley, Oliver","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","first_name":"Oliver"},{"first_name":"Nicola","full_name":"Del Giudice, Nicola","last_name":"Del Giudice"},{"last_name":"Kang","full_name":"Kang, Mihyun","first_name":"Mihyun"},{"first_name":"Philipp","last_name":"Sprüssel","full_name":"Sprüssel, Philipp"}],"publisher":"Electronic Journal of Combinatorics","status":"public","corr_author":"1","abstract":[{"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.","lang":"eng"}],"publication":"Electronic Journal of Combinatorics","file":[{"success":1,"checksum":"057c676dcee70236aa234d4ce6138c69","date_created":"2022-08-08T06:28:52Z","relation":"main_file","file_size":1768663,"creator":"dernst","access_level":"open_access","file_name":"2022_ElecJournCombinatorics_Cooley.pdf","file_id":"11742","date_updated":"2022-08-08T06:28:52Z","content_type":"application/pdf"}],"issue":"3","oa_version":"Published Version","article_processing_charge":"No","doi":"10.37236/10607","volume":29,"file_date_updated":"2022-08-08T06:28:52Z","language":[{"iso":"eng"}],"date_published":"2022-07-29T00:00:00Z","publication_identifier":{"eissn":["1077-8926"]},"article_number":"P3.27","_id":"11740","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-08-07T22:01:59Z","department":[{"_id":"MaKw"}],"quality_controlled":"1","title":"Phase transition in cohomology groups of non-uniform random simplicial complexes","tmp":{"image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)","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)"},"has_accepted_license":"1","citation":{"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>.","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>.","short":"O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics 29 (2022).","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.","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>","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>"},"acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","ddc":["510"],"publication_status":"published","scopus_import":"1","oa":1,"article_type":"original","license":"https://creativecommons.org/licenses/by-nd/4.0/","month":"07","intvolume":"        29","year":"2022","arxiv":1,"external_id":{"arxiv":["2005.07103"],"isi":["000836200300001"]}},{"month":"08","publication_status":"published","ddc":["500","516","514"],"alternative_title":["ISTA Thesis"],"oa":1,"year":"2022","_id":"11777","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-021-3"]},"ec_funded":1,"citation":{"ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology Austria, 2022.","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>.","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>.","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.","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>","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>"},"has_accepted_license":"1","date_created":"2022-08-10T15:51:19Z","title":"High-dimensional expansion and crossing numbers of simplicial complexes","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"oa_version":"Published Version","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."}],"corr_author":"1","status":"public","file":[{"relation":"supplementary_material","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","date_created":"2022-08-10T15:34:04Z","file_size":16828,"creator":"pwild","date_updated":"2022-08-10T15:34:04Z","file_name":"flags.py","file_id":"11780","access_level":"open_access","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","content_type":"text/x-python"},{"relation":"supplementary_material","date_created":"2022-08-10T15:34:10Z","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","file_id":"11781","file_name":"lowerbound.cpp","date_updated":"2022-08-10T15:34:10Z","access_level":"open_access","file_size":12226,"creator":"pwild","description":"Code for proof of Lemma 8.20 in Thesis","content_type":"text/x-c++src"},{"description":"Code for proof of Proposition 7.9 in Thesis","content_type":"text/x-python","file_size":3240,"creator":"pwild","file_name":"upperbound.py","date_updated":"2022-08-10T15:34:17Z","file_id":"11782","access_level":"open_access","relation":"supplementary_material","date_created":"2022-08-10T15:34:17Z","checksum":"4cf81455c49e5dec3b9b2e3980137eeb"},{"content_type":"application/pdf","file_size":5086282,"creator":"pwild","date_updated":"2022-08-11T16:08:33Z","file_name":"finalthesisPascalWildPDFA.pdf","file_id":"11809","access_level":"open_access","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","relation":"main_file","date_created":"2022-08-11T16:08:33Z","checksum":"4e96575b10cbe4e0d0db2045b2847774"},{"relation":"source_file","date_created":"2022-08-11T16:09:19Z","checksum":"92d94842a1fb6dca5808448137573b2e","content_type":"application/zip","file_size":18150068,"creator":"pwild","file_name":"ThesisSubmission.zip","date_updated":"2022-08-11T16:09:19Z","file_id":"11810","access_level":"closed"}],"date_published":"2022-08-11T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2022-08-11T16:09:19Z","page":"170","article_processing_charge":"No","doi":"10.15479/at:ista:11777","date_updated":"2026-04-07T14:18:26Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"11","supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"author":[{"id":"4C20D868-F248-11E8-B48F-1D18A9856A87","first_name":"Pascal","last_name":"Wild","full_name":"Wild, Pascal"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","degree_awarded":"PhD"},{"type":"journal_article","author":[{"full_name":"Bossmann, Lea","last_name":"Bossmann","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","orcid":"0000-0002-6854-1343"}],"publisher":"AIP Publishing","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"isi":1,"day":"10","date_updated":"2025-04-14T07:43:58Z","doi":"10.1063/5.0089983","article_processing_charge":"Yes (via OA deal)","volume":63,"file_date_updated":"2022-08-11T07:03:02Z","date_published":"2022-06-10T00:00:00Z","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","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."}],"corr_author":"1","publication":"Journal of Mathematical Physics","file":[{"creator":"dernst","file_size":5957888,"access_level":"open_access","file_id":"11784","file_name":"2022_JourMathPhysics_Bossmann.pdf","date_updated":"2022-08-11T07:03:02Z","content_type":"application/pdf","success":1,"date_created":"2022-08-11T07:03:02Z","checksum":"d0d32c338c1896680174be88c70968fa","relation":"main_file"}],"issue":"6","oa_version":"Published Version","date_created":"2022-08-11T06:37:52Z","department":[{"_id":"RoSe"}],"quality_controlled":"1","title":"Low-energy spectrum and dynamics of the weakly interacting Bose gas","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","citation":{"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>.","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>.","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>","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>","ista":"Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting Bose gas. Journal of Mathematical Physics. 63(6), 061102.","short":"L. Bossmann, Journal of Mathematical Physics 63 (2022)."},"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"article_number":"061102","ec_funded":1,"_id":"11783","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        63","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"year":"2022","arxiv":1,"external_id":{"arxiv":["2203.00730"],"isi":["000809648100002"]},"ddc":["530"],"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.","publication_status":"published","article_type":"original","oa":1,"scopus_import":"1","month":"06"},{"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772242"]},"article_number":"1","_id":"11808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_created":"2022-08-11T14:35:52Z","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.SAND.2022.1","open_access":"1"}],"quality_controlled":"1","title":"Recent advances in fully dynamic graph algorithms","citation":{"mla":"Hanauer, Kathrin, et al. “Recent Advances in Fully Dynamic Graph Algorithms.” <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, vol. 221, 1, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">10.4230/LIPIcs.SAND.2022.1</a>.","chicago":"Hanauer, Kathrin, Monika Henzinger, and Christian Schulz. “Recent Advances in Fully Dynamic Graph Algorithms.” In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Vol. 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">https://doi.org/10.4230/LIPIcs.SAND.2022.1</a>.","ieee":"K. Hanauer, M. Henzinger, and C. Schulz, “Recent advances in fully dynamic graph algorithms,” in <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Virtual, 2022, vol. 221.","ama":"Hanauer K, Henzinger M, Schulz C. Recent advances in fully dynamic graph algorithms. In: <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>. Vol 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">10.4230/LIPIcs.SAND.2022.1</a>","apa":"Hanauer, K., Henzinger, M., &#38; Schulz, C. (2022). Recent advances in fully dynamic graph algorithms. In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i> (Vol. 221). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.1\">https://doi.org/10.4230/LIPIcs.SAND.2022.1</a>","ista":"Hanauer K, Henzinger M, Schulz C. 2022. Recent advances in fully dynamic graph algorithms. 1st Symposium on Algorithmic Foundations of Dynamic Networks. SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 221, 1.","short":"K. Hanauer, M. Henzinger, C. Schulz, in:, 1st Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022."},"publication_status":"published","scopus_import":"1","oa":1,"alternative_title":["LIPIcs"],"month":"04","intvolume":"       221","year":"2022","external_id":{"arxiv":["2102.11169"]},"arxiv":1,"day":"29","date_updated":"2024-11-06T08:23:49Z","type":"conference","author":[{"first_name":"Kathrin","last_name":"Hanauer","full_name":"Hanauer, Kathrin"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Schulz","full_name":"Schulz, Christian","first_name":"Christian"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","abstract":[{"text":"In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms.","lang":"eng"}],"publication":"1st Symposium on Algorithmic Foundations of Dynamic Networks","conference":{"end_date":"2022-03-30","name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks","location":"Virtual","start_date":"2022-03-28"},"oa_version":"Published Version","article_processing_charge":"No","doi":"10.4230/LIPIcs.SAND.2022.1","volume":221,"date_published":"2022-04-29T00:00:00Z","language":[{"iso":"eng"}]},{"type":"conference","author":[{"last_name":"Hanauer","full_name":"Hanauer, Kathrin","first_name":"Kathrin"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Hua, Qi Cheng","last_name":"Hua","first_name":"Qi Cheng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"29","date_updated":"2024-11-06T08:22:47Z","volume":221,"article_processing_charge":"No","doi":"10.4230/LIPIcs.SAND.2022.18","language":[{"iso":"eng"}],"date_published":"2022-04-29T00:00:00Z","publication":"1st Symposium on Algorithmic Foundations of Dynamic Networks","abstract":[{"lang":"eng","text":"This paper presents a comprehensive study of algorithms for maintaining the number of all connected four-vertex subgraphs in a dynamic graph. Specifically, our algorithms maintain the number of paths of length three in deterministic amortized O(m^{1/2}) update time, and any other connected four-vertex subgraph which is not a clique in deterministic amortized update time O(m^{2/3}). Queries can be answered in constant time. We also study the query times for subgraphs containing an arbitrary edge that is supplied only with the query as well as the case where only subgraphs containing a vertex s that is fixed beforehand are considered. For length-3 paths, paws, 4-cycles, and diamonds our bounds match or are not far from (conditional) lower bounds: Based on the OMv conjecture we show that any dynamic algorithm that detects the existence of paws, diamonds, or 4-cycles or that counts length-3 paths takes update time Ω(m^{1/2-δ}).\r\nAdditionally, for 4-cliques and all connected induced subgraphs, we show a lower bound of Ω(m^{1-δ}) for any small constant δ > 0 for the amortized update time, assuming the static combinatorial 4-clique conjecture holds. This shows that the O(m) algorithm by Eppstein et al. [David Eppstein et al., 2012] for these subgraphs cannot be improved by a polynomial factor."}],"status":"public","oa_version":"Published Version","conference":{"end_date":"2022-04-30","start_date":"2022-04-28","location":"Virtual","name":"SAND: Symposium on Algorithmic Foundations of Dynamic Networks"},"title":"Fully dynamic four-vertex subgraph counting","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.SAND.2022.18","open_access":"1"}],"date_created":"2022-08-12T06:57:55Z","extern":"1","citation":{"short":"K. Hanauer, M. Henzinger, Q.C. Hua, in:, 1st Symposium on Algorithmic Foundations of Dynamic Networks, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ista":"Hanauer K, Henzinger M, Hua QC. 2022. Fully dynamic four-vertex subgraph counting. 1st Symposium on Algorithmic Foundations of Dynamic Networks. SAND: Symposium on Algorithmic Foundations of Dynamic Networks, LIPIcs, vol. 221, 18.","apa":"Hanauer, K., Henzinger, M., &#38; Hua, Q. C. (2022). Fully dynamic four-vertex subgraph counting. In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i> (Vol. 221). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">https://doi.org/10.4230/LIPIcs.SAND.2022.18</a>","ama":"Hanauer K, Henzinger M, Hua QC. Fully dynamic four-vertex subgraph counting. In: <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>. Vol 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">10.4230/LIPIcs.SAND.2022.18</a>","ieee":"K. Hanauer, M. Henzinger, and Q. C. Hua, “Fully dynamic four-vertex subgraph counting,” in <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Virtual, 2022, vol. 221.","chicago":"Hanauer, Kathrin, Monika Henzinger, and Qi Cheng Hua. “Fully Dynamic Four-Vertex Subgraph Counting.” In <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, Vol. 221. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">https://doi.org/10.4230/LIPIcs.SAND.2022.18</a>.","mla":"Hanauer, Kathrin, et al. “Fully Dynamic Four-Vertex Subgraph Counting.” <i>1st Symposium on Algorithmic Foundations of Dynamic Networks</i>, vol. 221, 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SAND.2022.18\">10.4230/LIPIcs.SAND.2022.18</a>."},"article_number":"18","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772242"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11812","intvolume":"       221","arxiv":1,"external_id":{"arxiv":["2106.15524"]},"year":"2022","alternative_title":["LIPIcs"],"scopus_import":"1","oa":1,"publication_status":"published","month":"04"},{"intvolume":"       119","external_id":{"pmid":["35901206"],"isi":["000903753500002"]},"year":"2022","scopus_import":"1","article_type":"original","oa":1,"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).","ddc":["570"],"publication_status":"published","month":"07","title":"Adsorption free energy predicts amyloid protein nucleation rates","department":[{"_id":"AnSa"}],"quality_controlled":"1","date_created":"2022-08-14T22:01:45Z","citation":{"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>.","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.","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>.","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>","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>","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).","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."},"pmid":1,"has_accepted_license":"1","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)"},"ec_funded":1,"article_number":"e2109718119","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11841","volume":119,"doi":"10.1073/pnas.2109718119","article_processing_charge":"No","date_published":"2022-07-28T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2023-10-04T09:05:44Z","issue":"31","file":[{"content_type":"application/pdf","creator":"dernst","file_size":2476021,"date_updated":"2023-10-04T09:05:44Z","file_id":"14386","file_name":"2022_PNAS_Toprakcioglu.pdf","access_level":"open_access","relation":"main_file","date_created":"2023-10-04T09:05:44Z","checksum":"0fe3878896cbeb6c44e29222ec2f336a","success":1}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","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"}],"status":"public","oa_version":"Published Version","type":"journal_article","author":[{"first_name":"Zenon","full_name":"Toprakcioglu, Zenon","last_name":"Toprakcioglu"},{"last_name":"Kamada","full_name":"Kamada, Ayaka","first_name":"Ayaka"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"first_name":"Mengqi","full_name":"Xie, Mengqi","last_name":"Xie"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Wei","full_name":"Wei, Jiapeng","first_name":"Jiapeng"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."}],"publisher":"National Academy of Sciences","day":"28","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"isi":1,"date_updated":"2025-06-12T06:21:34Z"},{"publication":"Journal of Mathematical Fluid Mechanics","file":[{"date_created":"2022-08-16T06:55:22Z","checksum":"75c5f286300e6f0539cf57b4dba108d5","relation":"main_file","success":1,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_JMathFluidMech_Hensel.pdf","date_updated":"2022-08-16T06:55:22Z","file_id":"11848","file_size":2045570,"creator":"cchlebak"}],"issue":"3","status":"public","abstract":[{"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.","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","volume":24,"article_processing_charge":"No","doi":"10.1007/s00021-022-00722-2","file_date_updated":"2022-08-16T06:55:22Z","language":[{"iso":"eng"}],"date_published":"2022-08-01T00:00:00Z","day":"01","project":[{"call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"isi":1,"date_updated":"2026-04-07T13:28:13Z","type":"journal_article","publisher":"Springer Nature","author":[{"full_name":"Hensel, Sebastian","last_name":"Hensel","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072"},{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio","full_name":"Marveggio, Alice"}],"scopus_import":"1","article_type":"original","oa":1,"publication_status":"published","ddc":["510"],"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.","month":"08","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14587"}]},"intvolume":"        24","year":"2022","external_id":{"arxiv":["2112.11154"],"isi":["000834834300001"]},"arxiv":1,"article_number":"93","ec_funded":1,"publication_identifier":{"eissn":["1422-6952"],"issn":["1422-6928"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11842","department":[{"_id":"JuFi"}],"quality_controlled":"1","title":"Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities","date_created":"2022-08-14T22:01:45Z","has_accepted_license":"1","citation":{"short":"S. Hensel, A. Marveggio, Journal of Mathematical Fluid Mechanics 24 (2022).","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.","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>","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>","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.","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>.","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>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"oa_version":"Published Version","conference":{"location":"Salerno, Italy","start_date":"2022-07-25","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2022-07-29"},"file":[{"content_type":"application/pdf","file_size":1593474,"creator":"cchlebak","access_level":"open_access","date_updated":"2022-08-16T08:05:15Z","file_id":"11854","file_name":"2022_PODC_Alistarh.pdf","date_created":"2022-08-16T08:05:15Z","checksum":"4c6b29172b8e355b4fbc364a2e0827b2","relation":"main_file","success":1}],"publication":"Proceedings of the Annual ACM Symposium on Principles of Distributed Computing","status":"public","corr_author":"1","abstract":[{"lang":"eng","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."}],"file_date_updated":"2022-08-16T08:05:15Z","date_published":"2022-07-21T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1145/3519270.3538435","article_processing_charge":"Yes (via OA deal)","page":"246-256","date_updated":"2025-12-30T09:04:17Z","day":"21","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"author":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"orcid":"0000-0002-6432-6646","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","last_name":"Rybicki"},{"first_name":"Sasha","last_name":"Voitovych","full_name":"Voitovych, Sasha"}],"publisher":"Association for Computing Machinery","type":"conference","month":"07","oa":1,"scopus_import":"1","ddc":["000"],"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).","publication_status":"published","year":"2022","external_id":{"isi":["001031439100030"],"arxiv":["2205.12597"]},"arxiv":1,"related_material":{"record":[{"id":"19969","relation":"later_version","status":"public"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"11844","ec_funded":1,"publication_identifier":{"isbn":["9781450392624"]},"has_accepted_license":"1","citation":{"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>","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>","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.","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.","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>.","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>.","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."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","department":[{"_id":"DaAl"}],"title":"Near-optimal leader election in population protocols on graphs","date_created":"2022-08-14T22:01:46Z"},{"year":"2022","external_id":{"isi":["000809108500001"]},"keyword":["Mathematics (miscellaneous)"],"intvolume":"        22","month":"06","oa":1,"article_type":"original","scopus_import":"1","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).","ddc":["510"],"publication_status":"published","has_accepted_license":"1","citation":{"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>.","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.","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>.","ista":"Agresti A, Veraar M. 2022. Nonlinear parabolic stochastic evolution equations in critical spaces part II. Journal of Evolution Equations. 22(2), 56.","short":"A. Agresti, M. Veraar, Journal of Evolution Equations 22 (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>","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>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"JuFi"}],"quality_controlled":"1","title":"Nonlinear parabolic stochastic evolution equations in critical spaces part II","date_created":"2022-08-16T08:39:43Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11858","article_number":"56","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"file_date_updated":"2022-08-16T08:52:46Z","language":[{"iso":"eng"}],"date_published":"2022-06-01T00:00:00Z","volume":22,"doi":"10.1007/s00028-022-00786-7","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","file":[{"success":1,"relation":"main_file","checksum":"59b99d1b48b6bd40983e7ce298524a21","date_created":"2022-08-16T08:52:46Z","file_name":"2022_Journal of Evolution Equations_Agresti.pdf","file_id":"11862","date_updated":"2022-08-16T08:52:46Z","access_level":"open_access","creator":"kschuh","file_size":1758371,"content_type":"application/pdf"}],"publication":"Journal of Evolution Equations","issue":"2","status":"public","abstract":[{"lang":"eng","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."}],"corr_author":"1","author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti","full_name":"Agresti, Antonio"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"publisher":"Springer Nature","type":"journal_article","date_updated":"2024-10-09T21:03:06Z","day":"01","isi":1}]