[{"author":[{"orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"}],"date_created":"2020-12-09T15:04:02Z","oa":1,"file":[{"creator":"bkavcic","file_id":"8932","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","date_created":"2020-12-09T15:00:19Z","date_updated":"2020-12-09T15:00:19Z","access_level":"open_access","relation":"main_file","file_name":"PLoSCompBiol2020_datarep.zip","success":1,"content_type":"application/zip","file_size":315494370}],"month":"12","article_processing_charge":"No","citation":{"chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>","short":"B. Kavcic, (2020).","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"GaTk"}],"file_date_updated":"2020-12-09T15:00:19Z","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930","has_accepted_license":"1","related_material":{"record":[{"id":"8997","status":"public","relation":"used_in_publication"}]},"date_updated":"2025-06-12T06:33:18Z","status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"type":"research_data","corr_author":"1","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"day":"10","contributor":[{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","contributor_type":"supervisor","orcid":"0000-0002-6699-1455"},{"first_name":"Tobias","last_name":"Bollenbach","contributor_type":"supervisor","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"_id":"8930","oa_version":"Published Version","year":"2020"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}],"department":[{"_id":"JoFi"}],"title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","author":[{"first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopčík, M.","last_name":"Kopčík","first_name":"M."},{"first_name":"P.","last_name":"Szabó","full_name":"Szabó, P."},{"first_name":"T.","full_name":"Samuely, T.","last_name":"Samuely"},{"full_name":"Kačmarčík, J.","last_name":"Kačmarčík","first_name":"J."},{"last_name":"Neilinger","full_name":"Neilinger, P.","first_name":"P."},{"full_name":"Grajcar, M.","first_name":"M.","last_name":"Grajcar"},{"last_name":"Samuely","first_name":"P.","full_name":"Samuely, P."}],"external_id":{"arxiv":["2011.04329"],"isi":["000591509900003"]},"issue":"18","publication":"Physical Review B","day":"01","abstract":[{"text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2.","lang":"eng"}],"oa_version":"Preprint","article_number":"180508","publication_status":"published","scopus_import":"1","volume":102,"month":"11","article_processing_charge":"No","oa":1,"citation":{"ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>","chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020.","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020)."},"date_published":"2020-11-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"quality_controlled":"1","date_created":"2020-12-13T23:01:21Z","arxiv":1,"article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8944","year":"2020","doi":"10.1103/PhysRevB.102.180508","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","type":"journal_article","status":"public","publisher":"American Physical Society","date_updated":"2025-07-10T12:01:27Z","intvolume":"       102"},{"file":[{"date_created":"2020-12-14T08:09:43Z","access_level":"open_access","relation":"main_file","date_updated":"2020-12-14T08:09:43Z","creator":"dernst","file_id":"8950","checksum":"5095cbdc728c9a510c5761cf60a8861c","file_name":"2020_Cells_Zhang.pdf","success":1,"file_size":3504525,"content_type":"application/pdf"}],"department":[{"_id":"SiHi"}],"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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","author":[{"full_name":"Zhang, Xuying","last_name":"Zhang","first_name":"Xuying"},{"last_name":"Mennicke","full_name":"Mennicke, Christine V.","first_name":"Christine V."},{"full_name":"Xiao, Guanxi","last_name":"Xiao","first_name":"Guanxi"},{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","last_name":"Beattie"},{"last_name":"Haider","first_name":"Mansoor","full_name":"Haider, Mansoor"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"last_name":"Ghashghaei","first_name":"H. Troy","full_name":"Ghashghaei, H. Troy"}],"external_id":{"pmid":["33322301"],"isi":["000601787300001"]},"issue":"12","publication":"Cells","project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"abstract":[{"lang":"eng","text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>"}],"ddc":["570"],"day":"11","ec_funded":1,"oa_version":"Published Version","article_number":"2662","has_accepted_license":"1","publication_status":"published","scopus_import":"1","volume":9,"month":"12","article_processing_charge":"No","oa":1,"citation":{"chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662."},"file_date_updated":"2020-12-14T08:09:43Z","date_published":"2020-12-11T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2073-4409"]},"date_created":"2020-12-14T08:04:03Z","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8949","pmid":1,"year":"2020","doi":"10.3390/cells9122662","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","status":"public","publisher":"MDPI","type":"journal_article","date_updated":"2025-06-12T07:02:43Z","intvolume":"         9"},{"date_created":"2020-12-20T10:00:26Z","author":[{"orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","date_published":"2020-12-21T00:00:00Z","file_date_updated":"2020-12-20T22:01:44Z","citation":{"short":"A.A. Nagy-Staron, (2020).","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"CaGu"}],"oa":1,"file":[{"file_size":523,"content_type":"text/plain","success":1,"file_name":"readme.txt","access_level":"open_access","relation":"main_file","date_updated":"2020-12-20T09:52:52Z","date_created":"2020-12-20T09:52:52Z","file_id":"8952","creator":"bkavcic","checksum":"f57862aeee1690c7effd2b1117d40ed1"},{"success":1,"file_name":"GRNs Research depository.gb","checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","creator":"bkavcic","date_created":"2020-12-20T22:01:44Z","access_level":"open_access","relation":"main_file","date_updated":"2020-12-20T22:01:44Z","content_type":"application/octet-stream","file_size":379228}],"month":"12","article_processing_charge":"No","date_updated":"2025-06-12T06:36:16Z","type":"research_data","status":"public","corr_author":"1","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9283"}]},"doi":"10.15479/AT:ISTA:8951","oa_version":"Published Version","year":"2020","_id":"8951","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"contributor":[{"contributor_type":"project_member","first_name":"Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tomasek","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Kathrin"},{"first_name":"Caroline","last_name":"Caruso Carter","contributor_type":"project_member"},{"first_name":"Elisabeth","last_name":"Sonnleitner","contributor_type":"project_member"},{"orcid":"0000-0001-6041-254X","first_name":"Bor","contributor_type":"project_member","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","contributor_type":"project_member","last_name":"Paixão"},{"contributor_type":"project_manager","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}]},{"pmid":1,"year":"2020","_id":"8955","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"article_type":"original","intvolume":"        11","date_updated":"2025-04-14T07:43:50Z","type":"journal_article","status":"public","publisher":"Frontiers","doi":"10.3389/fphys.2020.558070","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","date_published":"2020-11-26T00:00:00Z","file_date_updated":"2020-12-21T10:37:50Z","citation":{"apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>.","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020)."},"oa":1,"volume":11,"month":"11","article_processing_charge":"No","date_created":"2020-12-20T23:01:18Z","quality_controlled":"1","publication_identifier":{"eissn":["1664042X"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","ec_funded":1,"abstract":[{"text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies.","lang":"eng"}],"day":"26","ddc":["570"],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"Frontiers in Physiology","scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"558070","title":"Network physiology of cortico–muscular interactions","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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"GaTk"}],"file":[{"success":1,"file_name":"2020_Frontiers_Rizzo.pdf","file_id":"8961","checksum":"ef9515b28c5619b7126c0f347958bcb3","creator":"dernst","date_created":"2020-12-21T10:37:50Z","date_updated":"2020-12-21T10:37:50Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":13380030}],"external_id":{"isi":["000596849400001"],"pmid":["33324233"]},"author":[{"first_name":"Rossella","full_name":"Rizzo, Rossella","last_name":"Rizzo"},{"first_name":"Xiyun","last_name":"Zhang","full_name":"Zhang, Xiyun"},{"full_name":"Wang, Jilin W.J.L.","last_name":"Wang","first_name":"Jilin W.J.L."},{"full_name":"Lombardi, Fabrizio","last_name":"Lombardi","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"first_name":"Plamen Ch","full_name":"Ivanov, Plamen Ch","last_name":"Ivanov"}]},{"title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","department":[{"_id":"CaHe"}],"external_id":{"pmid":["33207225"],"isi":["000600665700008"]},"author":[{"last_name":"Godard","full_name":"Godard, Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87","first_name":"Benoit G"},{"full_name":"Dumollard, Rémi","last_name":"Dumollard","first_name":"Rémi"},{"full_name":"Munro, Edwin","first_name":"Edwin","last_name":"Munro"},{"full_name":"Chenevert, Janet","first_name":"Janet","last_name":"Chenevert"},{"first_name":"Céline","full_name":"Hebras, Céline","last_name":"Hebras"},{"first_name":"Alex","last_name":"Mcdougall","full_name":"Mcdougall, Alex"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","abstract":[{"text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation.","lang":"eng"}],"day":"21","issue":"6","publication":"Developmental Cell","scopus_import":"1","corr_author":"1","publication_status":"published","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/relaxing-cell-divisions/","relation":"press_release"}]},"date_published":"2020-12-21T00:00:00Z","citation":{"apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., &#38; Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">https://doi.org/10.1016/j.devcel.2020.10.016</a>","ieee":"B. G. Godard <i>et al.</i>, “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” <i>Developmental Cell</i>, vol. 55, no. 6. Elsevier, pp. 695–706, 2020.","mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” <i>Developmental Cell</i>, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">10.1016/j.devcel.2020.10.016</a>.","chicago":"Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” <i>Developmental Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">https://doi.org/10.1016/j.devcel.2020.10.016</a>.","ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. <i>Developmental Cell</i>. 2020;55(6):695-706. doi:<a href=\"https://doi.org/10.1016/j.devcel.2020.10.016\">10.1016/j.devcel.2020.10.016</a>","ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706.","short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706."},"article_processing_charge":"No","volume":55,"month":"12","date_created":"2020-12-20T23:01:19Z","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"year":"2020","_id":"8957","acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}],"page":"695-706","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","intvolume":"        55","date_updated":"2025-07-10T12:01:28Z","type":"journal_article","publisher":"Elsevier","status":"public","doi":"10.1016/j.devcel.2020.10.016","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8)."},{"date_created":"2020-12-23T08:25:45Z","publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2020-12-22T00:00:00Z","file_date_updated":"2020-12-28T08:16:10Z","citation":{"short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>"},"volume":11,"month":"12","article_processing_charge":"No","oa":1,"intvolume":"        11","status":"public","type":"journal_article","publisher":"Springer Nature","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_updated":"2025-04-15T07:52:12Z","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","doi":"10.1038/s41467-020-20286-x","year":"2020","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"_id":"8971","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","isi":1,"external_id":{"isi":["000603078000003"]},"author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","orcid":"0000-0001-8370-6161"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_size":3958727,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-12-28T08:16:10Z","date_created":"2020-12-28T08:16:10Z","creator":"dernst","file_id":"8975","checksum":"55d43ea0061cc4027ba45e966e1db8cc","success":1,"file_name":"2020_NatureComm_Faessler.pdf"}],"scopus_import":"1","publication_status":"published","corr_author":"1","has_accepted_license":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage"}]},"article_number":"6437","oa_version":"Published Version","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","grant_number":"M02495"}],"abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"ddc":["570"],"day":"22","publication":"Nature Communications"},{"doi":"10.1214/20-EJP536","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","date_updated":"2025-04-14T07:43:50Z","publisher":" Institute of Mathematical Statistics","status":"public","type":"journal_article","intvolume":"        25","isi":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8973","year":"2020","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1083-6489"]},"arxiv":1,"date_created":"2020-12-27T23:01:17Z","oa":1,"volume":25,"article_processing_charge":"No","month":"10","citation":{"chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>.","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>. 2020;25. doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” <i>Electronic Journal of Probability</i>, vol. 25.  Institute of Mathematical Statistics, 2020.","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>, vol. 25, 138,  Institute of Mathematical Statistics, 2020, doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>.","apa":"Redig, F., Saada, E., &#38; Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138."},"file_date_updated":"2020-12-28T08:24:08Z","date_published":"2020-10-21T00:00:00Z","article_number":"138","has_accepted_license":"1","publication_status":"published","scopus_import":"1","publication":"Electronic Journal of Probability","day":"21","abstract":[{"text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity.","lang":"eng"}],"ddc":["510"],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa_version":"Published Version","author":[{"full_name":"Redig, Frank","first_name":"Frank","last_name":"Redig"},{"last_name":"Saada","full_name":"Saada, Ellen","first_name":"Ellen"},{"full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico","last_name":"Sau"}],"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"file":[{"file_size":696653,"content_type":"application/pdf","date_created":"2020-12-28T08:24:08Z","date_updated":"2020-12-28T08:24:08Z","access_level":"open_access","relation":"main_file","checksum":"d75359b9814e78d57c0a481b7cde3751","creator":"dernst","file_id":"8976","file_name":"2020_ElectronJProbab_Redig.pdf","success":1}],"department":[{"_id":"JaMa"}],"title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics"},{"quality_controlled":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"date_created":"2021-01-10T23:01:17Z","citation":{"chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>.","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(50):31614-31622. doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. <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.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>","short":"R. Grah, B. Zoller, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 31614–31622.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America. 117(50), 31614–31622."},"oa":1,"article_processing_charge":"No","month":"12","volume":117,"date_published":"2020-12-15T00:00:00Z","file_date_updated":"2021-01-11T08:37:31Z","doi":"10.1073/pnas.2006731117","acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","intvolume":"       117","date_updated":"2025-05-14T10:57:50Z","type":"journal_article","status":"public","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","year":"2020","pmid":1,"_id":"9000","page":"31614-31622","author":[{"full_name":"Grah, Rok","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","orcid":"0000-0003-2539-3560"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"external_id":{"isi":["000600608300015"],"pmid":["33268497"]},"department":[{"_id":"GaTk"}],"tmp":{"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)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"file":[{"content_type":"application/pdf","file_size":1199247,"checksum":"69039cd402a571983aa6cb4815ffa863","file_id":"9004","creator":"dernst","date_created":"2021-01-11T08:37:31Z","date_updated":"2021-01-11T08:37:31Z","access_level":"open_access","relation":"main_file","success":1,"file_name":"2020_PNAS_Grah.pdf"}],"title":"Nonequilibrium models of optimal enhancer function","has_accepted_license":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/"}]},"scopus_import":"1","publication_status":"published","corr_author":"1","day":"15","abstract":[{"text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.","lang":"eng"}],"ddc":["570"],"project":[{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"50","oa_version":"Published Version"},{"page":"635-659","_id":"9007","year":"2020","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"European Mathematical Society","type":"journal_article","date_updated":"2025-07-10T12:01:31Z","intvolume":"        95","doi":"10.4171/CMH/499","date_published":"2020-12-07T00:00:00Z","article_processing_charge":"No","month":"12","volume":95,"oa":1,"citation":{"ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","apa":"Browning, T. D., &#38; Sawin, W. (2020). Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>","ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4. European Mathematical Society, pp. 635–659, 2020.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4, European Mathematical Society, 2020, pp. 635–59, doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>.","ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. 2020;95(4):635-659. doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society, 2020. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>."},"date_created":"2021-01-17T23:01:11Z","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1420-8946"],"issn":["0010-2571"]},"oa_version":"Preprint","publication":"Commentarii Mathematici Helvetici","issue":"4","day":"07","abstract":[{"lang":"eng","text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals."}],"publication_status":"published","scopus_import":"1","title":"Free rational points on smooth hypersurfaces","main_file_link":[{"url":"https://arxiv.org/abs/1906.08463","open_access":"1"}],"department":[{"_id":"TiBr"}],"external_id":{"isi":["000596833300001"],"arxiv":["1906.08463"]},"author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177"},{"first_name":"Will","full_name":"Sawin, Will","last_name":"Sawin"}]},{"publication":"Proceedings of the VLDB Endowment","issue":"4","abstract":[{"lang":"eng","text":"Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.\r\n\r\nCalypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees."}],"day":"01","oa_version":"Published Version","corr_author":"1","publication_status":"published","scopus_import":"1","main_file_link":[{"url":"https://dl.acm.org/doi/10.14778/3436905.3436917","open_access":"1"}],"tmp":{"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)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"ElKo"}],"title":"CALYPSO: Private data management for decentralized ledgers","author":[{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Alp, Enis Ceyhun","first_name":"Enis Ceyhun","last_name":"Alp"},{"last_name":"Gasser","full_name":"Gasser, Linus","first_name":"Linus"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"},{"first_name":"Ewa","last_name":"Syta","full_name":"Syta, Ewa"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}],"external_id":{"isi":["000658495400012"]},"article_type":"original","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"586-599","_id":"9011","year":"2020","acknowledgement":"We thank Nicolas Gailly, Vincent Graf, Jean-Pierre Hubaux, Wouter Lueks, Massimo Marelli, Carmela Troncoso, Juan-Ramón Troncoso Pastoriza, Frédéric Pont, and Sandra Siby for their valuable feedback. This project was supported in part by the ETH domain under PHRT grant #2017−201, and by the AXA Research Fund, Byzgen, DFINITY, and the Swiss Data Science Center (SDSC).","doi":"10.14778/3436905.3436917","publisher":"Association for Computing Machinery","status":"public","type":"journal_article","date_updated":"2024-10-09T21:00:32Z","intvolume":"        14","month":"12","article_processing_charge":"No","volume":14,"oa":1,"citation":{"ama":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. 2020;14(4):586-599. doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>","chicago":"Kokoris Kogias, Eleftherios, Enis Ceyhun Alp, Linus Gasser, Philipp Jovanovic, Ewa Syta, and Bryan Ford. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>.","ieee":"E. Kokoris Kogias, E. C. Alp, L. Gasser, P. Jovanovic, E. Syta, and B. Ford, “CALYPSO: Private data management for decentralized ledgers,” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4. Association for Computing Machinery, pp. 586–599, 2020.","mla":"Kokoris Kogias, Eleftherios, et al. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4, Association for Computing Machinery, 2020, pp. 586–99, doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>.","apa":"Kokoris Kogias, E., Alp, E. C., Gasser, L., Jovanovic, P., Syta, E., &#38; Ford, B. (2020). CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>","short":"E. Kokoris Kogias, E.C. Alp, L. Gasser, P. Jovanovic, E. Syta, B. Ford, Proceedings of the VLDB Endowment 14 (2020) 586–599.","ista":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. 2020. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 14(4), 586–599."},"date_published":"2020-12-01T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2150-8097"]},"quality_controlled":"1","date_created":"2021-01-17T23:01:13Z"},{"citation":{"apa":"Fischer, J. L., Laux, T., &#38; Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>.","chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2020. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>.","ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(6):6222-6233. doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233.","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233."},"month":"12","article_processing_charge":"No","volume":52,"oa":1,"date_published":"2020-12-15T00:00:00Z","file_date_updated":"2021-01-25T07:48:39Z","quality_controlled":"1","publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"language":[{"iso":"eng"}],"date_created":"2021-01-24T23:01:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"year":"2020","page":"6222-6233","_id":"9039","doi":"10.1137/20M1322182","acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","intvolume":"        52","publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","status":"public","date_updated":"2025-07-10T12:01:32Z","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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"JuFi"}],"file":[{"file_name":"2020_SIAM_Fischer.pdf","success":1,"date_updated":"2021-01-25T07:48:39Z","relation":"main_file","access_level":"open_access","date_created":"2021-01-25T07:48:39Z","file_id":"9041","creator":"dernst","checksum":"21aa1cf4c30a86a00cae15a984819b5d","file_size":310655,"content_type":"application/pdf"}],"title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies","author":[{"first_name":"Julian L","full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","orcid":"0000-0002-0479-558X"},{"last_name":"Laux","first_name":"Tim","full_name":"Laux, Tim"},{"last_name":"Simon","full_name":"Simon, Theresa M.","first_name":"Theresa M."}],"external_id":{"isi":["000600695200027"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"abstract":[{"text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems.","lang":"eng"}],"ddc":["510"],"day":"15","issue":"6","publication":"SIAM Journal on Mathematical Analysis","oa_version":"Published Version","ec_funded":1,"has_accepted_license":"1","scopus_import":"1","corr_author":"1","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","page":"138-147","_id":"9040","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","doi":"10.34727/2020/isbn.978-3-85448-042-6_21","publisher":"TU Wien Academic Press","status":"public","type":"conference","date_updated":"2025-07-10T12:01:32Z","citation":{"apa":"Alamdari, P. A., Avni, G., Henzinger, T. A., &#38; Lukina, A. (2020). Formal methods with a touch of magic. In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i> (pp. 138–147). Online Conference: TU Wien Academic Press. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>","ieee":"P. A. Alamdari, G. Avni, T. A. Henzinger, and A. Lukina, “Formal methods with a touch of magic,” in <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, Online Conference, 2020, pp. 138–147.","mla":"Alamdari, Par Alizadeh, et al. “Formal Methods with a Touch of Magic.” <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, TU Wien Academic Press, 2020, pp. 138–47, doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>.","chicago":"Alamdari, Par Alizadeh, Guy Avni, Thomas A Henzinger, and Anna Lukina. “Formal Methods with a Touch of Magic.” In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, 138–47. TU Wien Academic Press, 2020. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>.","ama":"Alamdari PA, Avni G, Henzinger TA, Lukina A. Formal methods with a touch of magic. In: <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>. TU Wien Academic Press; 2020:138-147. doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>","ista":"Alamdari PA, Avni G, Henzinger TA, Lukina A. 2020. Formal methods with a touch of magic. Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 138–147.","short":"P.A. Alamdari, G. Avni, T.A. Henzinger, A. Lukina, in:, Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2020, pp. 138–147."},"month":"09","article_processing_charge":"No","oa":1,"date_published":"2020-09-21T00:00:00Z","file_date_updated":"2021-02-09T09:39:02Z","quality_controlled":"1","publication_identifier":{"isbn":["9783854480426"],"eissn":["2708-7824"]},"language":[{"iso":"eng"}],"conference":{"location":"Online Conference","start_date":"2020-09-21","end_date":"2020-09-24","name":"FMCAD: Formal Methods in Computer-Aided Design"},"date_created":"2021-01-24T23:01:10Z","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"day":"21","abstract":[{"lang":"eng","text":"Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training."}],"ddc":["000"],"publication":"Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design","oa_version":"Published Version","has_accepted_license":"1","scopus_import":"1","publication_status":"published","department":[{"_id":"ToHe"}],"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)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_name":"2020_FMCAD_Alamdari.pdf","success":1,"checksum":"d616d549a0ade78606b16f8a9540820f","creator":"dernst","file_id":"9109","date_updated":"2021-02-09T09:39:02Z","access_level":"open_access","relation":"main_file","date_created":"2021-02-09T09:39:02Z","content_type":"application/pdf","file_size":990999}],"title":"Formal methods with a touch of magic","author":[{"last_name":"Alamdari","full_name":"Alamdari, Par Alizadeh","first_name":"Par Alizadeh"},{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","full_name":"Lukina, Anna","last_name":"Lukina"}]},{"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2021-02-01T13:45:11Z","citation":{"mla":"Youssef, Mena, et al. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” <i>Soft Matter</i>, vol. 16, no. 17, Royal Society of Chemistry , 2020, pp. 4274–82, doi:<a href=\"https://doi.org/10.1039/c9sm01850f\">10.1039/c9sm01850f</a>.","ieee":"M. Youssef, A. Morin, A. Aubret, S. Sacanna, and J. A. Palacci, “Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt,” <i>Soft Matter</i>, vol. 16, no. 17. Royal Society of Chemistry , pp. 4274–4282, 2020.","apa":"Youssef, M., Morin, A., Aubret, A., Sacanna, S., &#38; Palacci, J. A. (2020). Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c9sm01850f\">https://doi.org/10.1039/c9sm01850f</a>","chicago":"Youssef, Mena, Alexandre Morin, Antoine Aubret, Stefano Sacanna, and Jérémie A Palacci. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” <i>Soft Matter</i>. Royal Society of Chemistry , 2020. <a href=\"https://doi.org/10.1039/c9sm01850f\">https://doi.org/10.1039/c9sm01850f</a>.","ama":"Youssef M, Morin A, Aubret A, Sacanna S, Palacci JA. Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. <i>Soft Matter</i>. 2020;16(17):4274-4282. doi:<a href=\"https://doi.org/10.1039/c9sm01850f\">10.1039/c9sm01850f</a>","short":"M. Youssef, A. Morin, A. Aubret, S. Sacanna, J.A. Palacci, Soft Matter 16 (2020) 4274–4282.","ista":"Youssef M, Morin A, Aubret A, Sacanna S, Palacci JA. 2020. Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. Soft Matter. 16(17), 4274–4282."},"volume":16,"month":"05","article_processing_charge":"No","date_published":"2020-05-07T00:00:00Z","doi":"10.1039/c9sm01850f","intvolume":"        16","status":"public","type":"journal_article","keyword":["General Chemistry","Condensed Matter Physics"],"publisher":"Royal Society of Chemistry ","date_updated":"2023-02-23T13:47:45Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"original","pmid":1,"year":"2020","page":"4274-4282","_id":"9054","author":[{"first_name":"Mena","full_name":"Youssef, Mena","last_name":"Youssef"},{"last_name":"Morin","full_name":"Morin, Alexandre","first_name":"Alexandre"},{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"},{"full_name":"Sacanna, Stefano","first_name":"Stefano","last_name":"Sacanna"},{"full_name":"Palacci, Jérémie A","first_name":"Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"}],"external_id":{"pmid":["32307507"]},"title":"Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt","scopus_import":"1","extern":"1","publication_status":"published","day":"07","abstract":[{"text":"The fundamental and practical importance of particle stabilization has motivated various characterization methods for studying polymer brushes on particle surfaces. In this work, we show how one can perform sensitive measurements of neutral polymer coating on colloidal particles using a commercial zetameter and salt solutions. By systematically varying the Debye length, we study the mobility of the polymer-coated particles in an applied electric field and show that the electrophoretic mobility of polymer-coated particles normalized by the mobility of non-coated particles is entirely controlled by the polymer brush and independent of the native surface charge, here controlled with pH, or the surface–ion interaction. Our result is rationalized with a simple hydrodynamic model, allowing for the estimation of characteristics of the polymer coating: the brush length L, and the Brinkman length ξ, determined by its resistance to flows. We demonstrate that the Debye layer provides a convenient and faithful probe to the characterization of polymer coatings on particles. Because the method simply relies on a conventional zetameter, it is widely accessible and offers a practical tool to rapidly probe neutral polymer brushes, an asset in the development and utilization of polymer-coated colloidal particles.","lang":"eng"}],"issue":"17","publication":"Soft Matter","oa_version":"None"},{"title":"Ionic solids from common colloids","external_id":{"pmid":["32322078"]},"author":[{"first_name":"Theodore","last_name":"Hueckel","full_name":"Hueckel, Theodore"},{"last_name":"Hocky","first_name":"Glen M.","full_name":"Hocky, Glen M."},{"orcid":"0000-0002-7253-9465","last_name":"Palacci","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"full_name":"Sacanna, Stefano","last_name":"Sacanna","first_name":"Stefano"}],"oa_version":"None","abstract":[{"lang":"eng","text":"From rock salt to nanoparticle superlattices, complex structure can emerge from simple building blocks that attract each other through Coulombic forces1-4. On the micrometre scale, however, colloids in water defy the intuitively simple idea of forming crystals from oppositely charged partners, instead forming non-equilibrium structures such as clusters and gels5-7. Although various systems have been engineered to grow binary crystals8-11, native surface charge in aqueous conditions has not been used to assemble crystalline materials. Here we form ionic colloidal crystals in water through an approach that we refer to as polymer-attenuated Coulombic self-assembly. The key to crystallization is the use of a neutral polymer to keep particles separated by well defined distances, allowing us to tune the attractive overlap of electrical double layers, directing particles to disperse, crystallize or become permanently fixed on demand. The nucleation and growth of macroscopic single crystals is demonstrated by using the Debye screening length to fine-tune assembly. Using a variety of colloidal particles and commercial polymers, ionic colloidal crystals isostructural to caesium chloride, sodium chloride, aluminium diboride and K4C60 are selected according to particle size ratios. Once fixed by simply diluting out solution salts, crystals are pulled out of the water for further manipulation, demonstrating an accurate translation from solution-phase assembly to dried solid structures. In contrast to other assembly approaches, in which particles must be carefully engineered to encode binding information12-18, polymer-attenuated Coulombic self-assembly enables conventional colloids to be used as model colloidal ions, primed for crystallization. "}],"day":"23","issue":"7804","publication":"Nature","scopus_import":"1","extern":"1","publication_status":"published","date_published":"2020-04-23T00:00:00Z","citation":{"ista":"Hueckel T, Hocky GM, Palacci JA, Sacanna S. 2020. Ionic solids from common colloids. Nature. 580(7804), 487–490.","short":"T. Hueckel, G.M. Hocky, J.A. Palacci, S. Sacanna, Nature 580 (2020) 487–490.","chicago":"Hueckel, Theodore, Glen M. Hocky, Jérémie A Palacci, and Stefano Sacanna. “Ionic Solids from Common Colloids.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2205-0\">https://doi.org/10.1038/s41586-020-2205-0</a>.","ama":"Hueckel T, Hocky GM, Palacci JA, Sacanna S. Ionic solids from common colloids. <i>Nature</i>. 2020;580(7804):487-490. doi:<a href=\"https://doi.org/10.1038/s41586-020-2205-0\">10.1038/s41586-020-2205-0</a>","apa":"Hueckel, T., Hocky, G. M., Palacci, J. A., &#38; Sacanna, S. (2020). Ionic solids from common colloids. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2205-0\">https://doi.org/10.1038/s41586-020-2205-0</a>","mla":"Hueckel, Theodore, et al. “Ionic Solids from Common Colloids.” <i>Nature</i>, vol. 580, no. 7804, Springer Nature, 2020, pp. 487–90, doi:<a href=\"https://doi.org/10.1038/s41586-020-2205-0\">10.1038/s41586-020-2205-0</a>.","ieee":"T. Hueckel, G. M. Hocky, J. A. Palacci, and S. Sacanna, “Ionic solids from common colloids,” <i>Nature</i>, vol. 580, no. 7804. Springer Nature, pp. 487–490, 2020."},"article_processing_charge":"No","volume":580,"month":"04","date_created":"2021-02-02T13:30:50Z","quality_controlled":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"pmid":1,"year":"2020","page":"487-490","_id":"9059","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"original","intvolume":"       580","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","publisher":"Springer Nature","date_updated":"2023-02-23T13:47:55Z","doi":"10.1038/s41586-020-2205-0"},{"publication_identifier":{"issn":["2046-2069"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2021-02-02T15:51:23Z","citation":{"ama":"Nauman M, Alnasir MH, Hamayun MA, Wang Y, Shatruk M, Manzoor S. Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. <i>RSC Advances</i>. 2020;10(47):28383-28389. doi:<a href=\"https://doi.org/10.1039/d0ra05394e\">10.1039/d0ra05394e</a>","chicago":"Nauman, Muhammad, Muhammad Hisham Alnasir, Muhammad Asif Hamayun, YiXu Wang, Michael Shatruk, and Sadia Manzoor. “Size-Dependent Magnetic and Magnetothermal Properties of Gadolinium Silicide Nanoparticles.” <i>RSC Advances</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0ra05394e\">https://doi.org/10.1039/d0ra05394e</a>.","apa":"Nauman, M., Alnasir, M. H., Hamayun, M. A., Wang, Y., Shatruk, M., &#38; Manzoor, S. (2020). Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. <i>RSC Advances</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0ra05394e\">https://doi.org/10.1039/d0ra05394e</a>","ieee":"M. Nauman, M. H. Alnasir, M. A. Hamayun, Y. Wang, M. Shatruk, and S. Manzoor, “Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles,” <i>RSC Advances</i>, vol. 10, no. 47. Royal Society of Chemistry, pp. 28383–28389, 2020.","mla":"Nauman, Muhammad, et al. “Size-Dependent Magnetic and Magnetothermal Properties of Gadolinium Silicide Nanoparticles.” <i>RSC Advances</i>, vol. 10, no. 47, Royal Society of Chemistry, 2020, pp. 28383–89, doi:<a href=\"https://doi.org/10.1039/d0ra05394e\">10.1039/d0ra05394e</a>.","ista":"Nauman M, Alnasir MH, Hamayun MA, Wang Y, Shatruk M, Manzoor S. 2020. Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. RSC Advances. 10(47), 28383–28389.","short":"M. Nauman, M.H. Alnasir, M.A. Hamayun, Y. Wang, M. Shatruk, S. Manzoor, RSC Advances 10 (2020) 28383–28389."},"month":"07","article_processing_charge":"No","volume":10,"oa":1,"date_published":"2020-07-29T00:00:00Z","DOAJ_listed":"1","doi":"10.1039/d0ra05394e","intvolume":"        10","publisher":"Royal Society of Chemistry","keyword":["General Chemistry","General Chemical Engineering"],"type":"journal_article","status":"public","date_updated":"2024-10-15T13:44:01Z","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","article_type":"original","OA_type":"gold","year":"2020","page":"28383-28389","_id":"9067","author":[{"orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman","first_name":"Muhammad","full_name":"Nauman, Muhammad"},{"full_name":"Alnasir, Muhammad Hisham","first_name":"Muhammad Hisham","last_name":"Alnasir"},{"first_name":"Muhammad Asif","last_name":"Hamayun","full_name":"Hamayun, Muhammad Asif"},{"full_name":"Wang, YiXu","last_name":"Wang","first_name":"YiXu"},{"full_name":"Shatruk, Michael","first_name":"Michael","last_name":"Shatruk"},{"last_name":"Manzoor","first_name":"Sadia","full_name":"Manzoor, Sadia"}],"main_file_link":[{"url":"https://doi.org/10.1039/d0ra05394e","open_access":"1"}],"title":"Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles","OA_place":"publisher","extern":"1","publication_status":"published","abstract":[{"text":"Gadolinium silicide (Gd5Si4) nanoparticles are an interesting class of materials due to their high magnetization, low Curie temperature, low toxicity in biological environments and their multifunctional properties. We report the magnetic and magnetothermal properties of gadolinium silicide (Gd5Si4) nanoparticles prepared by surfactant-assisted ball milling of arc melted bulk ingots of the compound. Using different milling times and speeds, a wide range of crystallite sizes (13–43 nm) could be produced and a reduction in Curie temperature (TC) from 340 K to 317 K was achieved, making these nanoparticles suitable for self-controlled magnetic hyperthermia applications. The magnetothermal effect was measured in applied AC magnetic fields of amplitude 164–239 Oe and frequencies 163–519 kHz. All particles showed magnetic heating with a strong dependence of the specific absorption rate (SAR) on the average crystallite size. The highest SAR of 3.7 W g−1 was measured for 43 nm sized nanoparticles of Gd5Si4. The high SAR and low TC, (within the therapeutic range for magnetothermal therapy) makes the Gd5Si4 behave like self-regulating heat switches that would be suitable for self-controlled magnetic hyperthermia applications after biocompatibility and cytotoxicity tests.","lang":"eng"}],"day":"29","publication":"RSC Advances","issue":"47","oa_version":"Published Version"},{"date_updated":"2021-02-04T07:21:35Z","keyword":["Electronic","Optical and Magnetic Materials","Surfaces","Coatings and Films","Polymers and Plastics","Metals and Alloys","Biomaterials"],"publication_status":"published","extern":"1","publisher":"IOP Publishing","type":"journal_article","status":"public","intvolume":"         6","article_number":"1250g6","doi":"10.1088/2053-1591/ab6886","_id":"9069","oa_version":"None","year":"2020","issue":"12","publication":"Materials Research Express","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","abstract":[{"text":"In the quest for alternate and efficient electrode materials, ternary metal electrocatalysts (TMEs), part of the perovskite family, were synthesized and tested for methanol electro-oxidation in alkaline media. La0.5Ca0.5MO3 (M = Ni, Co, or Mn) was synthesized via sol-gel method. X-ray diffraction analysis revealed that the perovskite crystal structure possesses characteristic sharp and crystalline peaks for all synthesized ternary electrocatalysts. The average particle size calculated using Debye–Scherrer equation was in the order of La0.5Ca0.5NiO3 (LCNO) > La0.5Ca0.5CoO3 (LCCO)> La0.5Ca0.5MnO3 (LCMO). The elemental composition of as prepared sample, LCCO was investigated via x-ray fluorescence spectroscopy. The qualitative and quantitative analysis revealed the presence of La, Ca and Co in parent crystal structure with percentage compositions of 9.0, 3.12 and 87.82% respectively. The particle size distribution was homogenous, as determined by scanning electron and transmission electron microscopes. The electrocatalytic activity of the synthesized ternary electrocatalysts was studied electrochemically by cyclic voltammetry. The calculated diffusion coefficient values showed that electrode surface of LCNO and LCCO have limited efficiency for diffusion related phenomenon. The heterogeneous rate constants inferred better electrode kinetics of LCCO and LCNO which exhibited good electrocatalytic behavior; sharp anodic peaks were observed in the potential range of +0.3 to 0.6 V and +0.6 to 0.8 V, respectively. Methanol electro-oxidation was found minimal in case of LCMO sample. We have observed that Co substitution at B-site of perovskite electrode materials attains better electrochemical properties, thus in relation with reported literature.","lang":"eng"}],"date_created":"2021-02-02T15:53:57Z","language":[{"iso":"eng"}],"author":[{"full_name":"Hussain, Tayyaba","first_name":"Tayyaba","last_name":"Hussain"},{"orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad","last_name":"Nauman"},{"first_name":"Sana","full_name":"Sabahat, Sana","last_name":"Sabahat"},{"full_name":"Arif, Saira","last_name":"Arif","first_name":"Saira"}],"publication_identifier":{"issn":["2053-1591"]},"quality_controlled":"1","title":"Synthesis of ternary electrocatalysts for exploration of methanol electro-oxidation in alkaline media","date_published":"2020-01-15T00:00:00Z","article_processing_charge":"No","month":"01","volume":6,"citation":{"apa":"Hussain, T., Nauman, M., Sabahat, S., &#38; Arif, S. (2020). Synthesis of ternary electrocatalysts for exploration of methanol electro-oxidation in alkaline media. <i>Materials Research Express</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2053-1591/ab6886\">https://doi.org/10.1088/2053-1591/ab6886</a>","mla":"Hussain, Tayyaba, et al. “Synthesis of Ternary Electrocatalysts for Exploration of Methanol Electro-Oxidation in Alkaline Media.” <i>Materials Research Express</i>, vol. 6, no. 12, 1250g6, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/2053-1591/ab6886\">10.1088/2053-1591/ab6886</a>.","ieee":"T. Hussain, M. Nauman, S. Sabahat, and S. Arif, “Synthesis of ternary electrocatalysts for exploration of methanol electro-oxidation in alkaline media,” <i>Materials Research Express</i>, vol. 6, no. 12. IOP Publishing, 2020.","chicago":"Hussain, Tayyaba, Muhammad Nauman, Sana Sabahat, and Saira Arif. “Synthesis of Ternary Electrocatalysts for Exploration of Methanol Electro-Oxidation in Alkaline Media.” <i>Materials Research Express</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/2053-1591/ab6886\">https://doi.org/10.1088/2053-1591/ab6886</a>.","ama":"Hussain T, Nauman M, Sabahat S, Arif S. Synthesis of ternary electrocatalysts for exploration of methanol electro-oxidation in alkaline media. <i>Materials Research Express</i>. 2020;6(12). doi:<a href=\"https://doi.org/10.1088/2053-1591/ab6886\">10.1088/2053-1591/ab6886</a>","ista":"Hussain T, Nauman M, Sabahat S, Arif S. 2020. Synthesis of ternary electrocatalysts for exploration of methanol electro-oxidation in alkaline media. Materials Research Express. 6(12), 1250g6.","short":"T. Hussain, M. Nauman, S. Sabahat, S. Arif, Materials Research Express 6 (2020)."}},{"type":"book_chapter","status":"public","publisher":"Springer Nature","publication_status":"published","date_updated":"2021-02-05T12:19:21Z","doi":"10.1007/978-3-319-90306-4_94-1","year":"2020","oa_version":"None","_id":"9096","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","publication":"Encyclopedia of Social Insects","date_created":"2021-02-05T12:15:18Z","publication_identifier":{"isbn":["9783319903064"]},"quality_controlled":"1","language":[{"iso":"eng"}],"author":[{"first_name":"Paul","full_name":"Schmid-Hempel, Paul","last_name":"Schmid-Hempel"},{"full_name":"Cremer, Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"}],"editor":[{"full_name":"Starr, C","last_name":"Starr","first_name":"C"}],"date_published":"2020-02-22T00:00:00Z","title":"Parasites and Pathogens","department":[{"_id":"SyCr"}],"citation":{"mla":"Schmid-Hempel, Paul, and Sylvia Cremer. “Parasites and Pathogens.” <i>Encyclopedia of Social Insects</i>, edited by C Starr, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">10.1007/978-3-319-90306-4_94-1</a>.","ieee":"P. Schmid-Hempel and S. Cremer, “Parasites and Pathogens,” in <i>Encyclopedia of Social Insects</i>, C. Starr, Ed. Cham: Springer Nature, 2020.","apa":"Schmid-Hempel, P., &#38; Cremer, S. (2020). Parasites and Pathogens. In C. Starr (Ed.), <i>Encyclopedia of Social Insects</i>. Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">https://doi.org/10.1007/978-3-319-90306-4_94-1</a>","ama":"Schmid-Hempel P, Cremer S. Parasites and Pathogens. In: Starr C, ed. <i>Encyclopedia of Social Insects</i>. Cham: Springer Nature; 2020. doi:<a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">10.1007/978-3-319-90306-4_94-1</a>","chicago":"Schmid-Hempel, Paul, and Sylvia Cremer. “Parasites and Pathogens.” In <i>Encyclopedia of Social Insects</i>, edited by C Starr. Cham: Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">https://doi.org/10.1007/978-3-319-90306-4_94-1</a>.","short":"P. Schmid-Hempel, S. Cremer, in:, C. Starr (Ed.), Encyclopedia of Social Insects, Springer Nature, Cham, 2020.","ista":"Schmid-Hempel P, Cremer S. 2020.Parasites and Pathogens. In: Encyclopedia of Social Insects. ."},"article_processing_charge":"No","month":"02","place":"Cham"},{"scopus_import":"1","publication_status":"published","oa_version":"Preprint","ec_funded":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"abstract":[{"text":"We consider the free additive convolution of two probability measures μ and ν on the real line and show that μ ⊞ v is supported on a single interval if μ and ν each has single interval support. Moreover, the density of μ ⊞ ν is proven to vanish as a square root near the edges of its support if both μ and ν have power law behavior with exponents between −1 and 1 near their edges. In particular, these results show the ubiquity of the conditions in our recent work on optimal local law at the spectral edges for addition of random matrices [5].","lang":"eng"}],"day":"01","publication":"Journal d'Analyse Mathematique","external_id":{"arxiv":["1804.11199"],"isi":["000611879400008"]},"author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0003-0954-3231","last_name":"Schnelli","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"}],"title":"On the support of the free additive convolution","department":[{"_id":"LaEr"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11199"}],"intvolume":"       142","publisher":"Springer Nature","status":"public","type":"journal_article","date_updated":"2025-07-10T12:01:37Z","acknowledgement":"Supported in part by Hong Kong RGC Grant ECS 26301517.\r\nSupported in part by ERC Advanced Grant RANMAT No. 338804.\r\nSupported in part by the Knut and Alice Wallenberg Foundation and the Swedish Research Council Grant VR-2017-05195.","doi":"10.1007/s11854-020-0135-2","year":"2020","page":"323-348","_id":"9104","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1,"date_created":"2021-02-07T23:01:15Z","arxiv":1,"publication_identifier":{"issn":["0021-7670"],"eissn":["1565-8538"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2020-11-01T00:00:00Z","citation":{"ista":"Bao Z, Erdös L, Schnelli K. 2020. On the support of the free additive convolution. Journal d’Analyse Mathematique. 142, 323–348.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal d’Analyse Mathematique 142 (2020) 323–348.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2020). On the support of the free additive convolution. <i>Journal d’Analyse Mathematique</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11854-020-0135-2\">https://doi.org/10.1007/s11854-020-0135-2</a>","mla":"Bao, Zhigang, et al. “On the Support of the Free Additive Convolution.” <i>Journal d’Analyse Mathematique</i>, vol. 142, Springer Nature, 2020, pp. 323–48, doi:<a href=\"https://doi.org/10.1007/s11854-020-0135-2\">10.1007/s11854-020-0135-2</a>.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “On the support of the free additive convolution,” <i>Journal d’Analyse Mathematique</i>, vol. 142. Springer Nature, pp. 323–348, 2020.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “On the Support of the Free Additive Convolution.” <i>Journal d’Analyse Mathematique</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11854-020-0135-2\">https://doi.org/10.1007/s11854-020-0135-2</a>.","ama":"Bao Z, Erdös L, Schnelli K. On the support of the free additive convolution. <i>Journal d’Analyse Mathematique</i>. 2020;142:323-348. doi:<a href=\"https://doi.org/10.1007/s11854-020-0135-2\">10.1007/s11854-020-0135-2</a>"},"article_processing_charge":"No","month":"11","volume":142,"oa":1},{"doi":"10.5194/essd-2020-269","date_updated":"2022-01-24T12:27:08Z","type":"preprint","publisher":"Copernicus Publications","status":"public","extern":"1","publication_status":"submitted","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"24","abstract":[{"lang":"eng","text":"The couplings among clouds, convection, and circulation in trade-wind regimes remain a fundamental puzzle that limits our ability to constrain future climate change. Radiative heating plays an important role in these couplings. Here we calculate the clear-sky radiative profiles from 2001 in-situ soundings (978 dropsondes and 1023 radiosondes) collected during the EUREC4A field campaign, which took place south and east of Barbados in January–February 2020. We describe the method used to calculate these radiative profiles and present preliminary results sampling variability at multiple scales, from the variability across all soundings to groupings by diurnal cycle and mesoscale organization state, as well as individual soundings associated with elevated moisture layers. This clear-sky radiative profiles data set can provide important missing detail to what can be learned from calculations based on passive remote sensing and help in investigating the role of radiation in dynamic and thermodynamic variability in trade-wind regimes. All data are archived and freely available for public access on AERIS (Albright et al. (2020), https://doi.org/10.25326/78)."}],"publication":"Earth System Science Data","oa_version":"Preprint","year":"2020","_id":"9124","language":[{"iso":"eng"}],"author":[{"last_name":"Albright","first_name":"Anna Lea","full_name":"Albright, Anna Lea"},{"first_name":"Benjamin","full_name":"Fildier, Benjamin","last_name":"Fildier"},{"first_name":"Ludovic","full_name":"Touzé-Peiffer, Ludovic","last_name":"Touzé-Peiffer"},{"full_name":"Pincus, Robert","last_name":"Pincus","first_name":"Robert"},{"first_name":"Jessica","last_name":"Vial","full_name":"Vial, Jessica"},{"last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"}],"date_created":"2021-02-15T14:05:54Z","citation":{"short":"A.L. Albright, B. Fildier, L. Touzé-Peiffer, R. Pincus, J. Vial, C.J. Muller, Earth System Science Data (n.d.).","ista":"Albright AL, Fildier B, Touzé-Peiffer L, Pincus R, Vial J, Muller CJ. Atmospheric radiative profiles during EUREC4A. Earth System Science Data, <a href=\"https://doi.org/10.5194/essd-2020-269\">10.5194/essd-2020-269</a>.","ama":"Albright AL, Fildier B, Touzé-Peiffer L, Pincus R, Vial J, Muller CJ. Atmospheric radiative profiles during EUREC4A. <i>Earth System Science Data</i>. doi:<a href=\"https://doi.org/10.5194/essd-2020-269\">10.5194/essd-2020-269</a>","chicago":"Albright, Anna Lea, Benjamin Fildier, Ludovic Touzé-Peiffer, Robert Pincus, Jessica Vial, and Caroline J Muller. “Atmospheric Radiative Profiles during EUREC4A.” <i>Earth System Science Data</i>. Copernicus Publications, n.d. <a href=\"https://doi.org/10.5194/essd-2020-269\">https://doi.org/10.5194/essd-2020-269</a>.","ieee":"A. L. Albright, B. Fildier, L. Touzé-Peiffer, R. Pincus, J. Vial, and C. J. Muller, “Atmospheric radiative profiles during EUREC4A,” <i>Earth System Science Data</i>. Copernicus Publications.","mla":"Albright, Anna Lea, et al. “Atmospheric Radiative Profiles during EUREC4A.” <i>Earth System Science Data</i>, Copernicus Publications, doi:<a href=\"https://doi.org/10.5194/essd-2020-269\">10.5194/essd-2020-269</a>.","apa":"Albright, A. L., Fildier, B., Touzé-Peiffer, L., Pincus, R., Vial, J., &#38; Muller, C. J. (n.d.). Atmospheric radiative profiles during EUREC4A. <i>Earth System Science Data</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/essd-2020-269\">https://doi.org/10.5194/essd-2020-269</a>"},"oa":1,"month":"09","main_file_link":[{"url":"https://doi.org/10.5194/essd-2020-269","open_access":"1"}],"article_processing_charge":"No","title":"Atmospheric radiative profiles during EUREC4A","date_published":"2020-09-24T00:00:00Z"}]