[{"conference":{"end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification","start_date":"2023-07-17"},"quality_controlled":"1","date_created":"2023-09-03T22:01:16Z","citation":{"ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 156–169.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>.","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>."},"oa":1,"title":"Lincheck: A practical framework for testing concurrent data structures on JVM","page":"156-169","date_published":"2023-07-17T00:00:00Z","intvolume":"     13964","has_accepted_license":"1","volume":13964,"day":"17","publication":"35th International Conference on Computer Aided Verification ","article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-09-06T08:16:25Z","doi":"10.1007/978-3-031-37706-8_8","_id":"14260","publication_status":"published","alternative_title":["LNCS"],"oa_version":"Published Version","ddc":["000"],"type":"conference","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2023-09-06T08:16:25Z","success":1,"checksum":"c346016393123a0a2338ad4d976f61bc","file_size":421408,"date_created":"2023-09-06T08:16:25Z","file_name":"2023_LNCS_Koval.pdf","file_id":"14275","creator":"dernst","relation":"main_file"}],"publisher":"Springer Nature","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"month":"07","year":"2023","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377051"],"issn":["0302-9743"]},"scopus_import":"1","abstract":[{"text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness.","lang":"eng"}],"related_material":{"record":[{"id":"14995","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-27T07:46:52Z","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita"},{"last_name":"Fedorov","full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander"},{"full_name":"Sokolova, Maria","last_name":"Sokolova","first_name":"Maria"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","date_created":"2023-09-06T08:07:51Z","citation":{"mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>"},"quality_controlled":"1","oa":1,"article_number":"adc9584","ec_funded":1,"article_processing_charge":"No","doi":"10.1126/sciimmunol.adc9584","intvolume":"         8","date_published":"2023-09-01T00:00:00Z","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","publication":"Science Immunology","day":"01","volume":8,"pmid":1,"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"article_type":"original","publication_identifier":{"issn":["2470-9468"]},"isi":1,"project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020"},{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"month":"09","year":"2023","oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"publication_status":"published","_id":"14274","issue":"87","publisher":"American Association for the Advancement of Science","status":"public","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko","full_name":"Alanko, Jonna H"},{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola"},{"last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","last_name":"Schwarz"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"related_material":{"record":[{"id":"14279","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14697"}]},"keyword":["General Medicine","Immunology"],"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-12-21T14:30:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"oa":1,"article_number":"013001","quality_controlled":"1","date_created":"2023-09-06T08:30:59Z","citation":{"mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>.","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>.","apa":"Boocock, D. R., Hirashima, T., &#38; Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” <i>PRX Life</i>, vol. 1, no. 1. American Physical Society, 2023.","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. 2023;1(1). doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>"},"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","day":"20","publication":"PRX Life","acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","volume":1,"date_published":"2023-07-20T00:00:00Z","intvolume":"         1","has_accepted_license":"1","file_date_updated":"2023-09-15T06:30:50Z","doi":"10.1103/prxlife.1.013001","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","ec_funded":1,"publisher":"American Physical Society","publication_status":"published","_id":"14277","issue":"1","oa_version":"Published Version","file":[{"relation":"main_file","creator":"dernst","file_id":"14335","file_name":"2023_PRXLife_Boocock.pdf","date_created":"2023-09-15T06:30:50Z","success":1,"checksum":"f881d98c89eb9f1aa136d7b781511553","file_size":2559520,"date_updated":"2023-09-15T06:30:50Z","content_type":"application/pdf","access_level":"open_access"}],"type":"journal_article","ddc":["570"],"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"year":"2023","month":"07","publication_identifier":{"issn":["2835-8279"]},"article_type":"original","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-09-15T06:39:17Z","abstract":[{"text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels.","lang":"eng"}],"status":"public","author":[{"full_name":"Boocock, Daniel R","last_name":"Boocock","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}]},{"article_processing_charge":"No","author":[{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","doi":"10.5281/ZENODO.8133960","abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14274"}]},"date_published":"2023-07-11T00:00:00Z","date_updated":"2023-10-03T11:42:58Z","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","department":[{"_id":"EdHa"}],"month":"07","year":"2023","date_created":"2023-09-06T08:39:25Z","citation":{"mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.”</i> Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","short":"M.C. Ucar, (2023).","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023."},"type":"research_data_reference","ddc":["570"],"oa_version":"Published Version","_id":"14279","publisher":"Zenodo","oa":1},{"year":"2023","month":"09","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall sythesis"}],"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"publisher":"Institute of Science and Technology Austria","_id":"14280","alternative_title":["ISTA Thesis"],"publication_status":"published","file":[{"file_size":114932847,"checksum":"87eef11fbc5c7df0826f12a3a629b444","date_created":"2023-10-04T10:11:53Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2023-10-04T10:28:35Z","creator":"pradler","file_id":"14390","relation":"source_file","file_name":"PhD Thesis_Philipp Radler_20231004.docx"},{"relation":"main_file","creator":"pradler","file_id":"14391","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_created":"2023-10-04T10:11:21Z","embargo_to":"open_access","checksum":"3253e099b7126469d941fd9419d68b4f","file_size":37838778,"date_updated":"2023-10-04T10:28:35Z","content_type":"application/pdf","embargo":"2024-10-04","access_level":"closed"}],"ddc":["572"],"oa_version":"Published Version","type":"dissertation","author":[{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler"}],"status":"public","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-02-21T12:35:18Z","abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11373"},{"id":"7387","relation":"part_of_dissertation","status":"public"},{"relation":"research_data","status":"public","id":"10934"}]},"page":"156","title":"Spatiotemporal signaling during assembly of the bacterial divisome","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_created":"2023-09-06T10:58:25Z","citation":{"ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>."},"file_date_updated":"2023-10-04T10:28:35Z","doi":"10.15479/at:ista:14280","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"25","date_published":"2023-09-25T00:00:00Z","degree_awarded":"PhD","has_accepted_license":"1"},{"month":"04","year":"2023","publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"isi":1,"article_type":"original","department":[{"_id":"TiBr"}],"publisher":"Oxford Academic","external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"publication_status":"published","issue":"8","_id":"9034","type":"journal_article","oa_version":"Preprint","status":"public","author":[{"last_name":"Wilsch","full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-01T12:23:55Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.08503"}],"abstract":[{"text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.","lang":"eng"}],"page":"6780-6808","title":"Integral points of bounded height on a log Fano threefold","oa":1,"quality_controlled":"1","arxiv":1,"date_created":"2021-01-22T09:31:09Z","citation":{"short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” <i>International Mathematics Research Notices</i>, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. <i>International Mathematics Research Notices</i>. 2023;2023(8):6780-6808. doi:<a href=\"https://doi.org/10.1093/imrn/rnac048\">10.1093/imrn/rnac048</a>","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” <i>International Mathematics Research Notices</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/imrn/rnac048\">https://doi.org/10.1093/imrn/rnac048</a>.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. <i>International Mathematics Research Notices</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/imrn/rnac048\">https://doi.org/10.1093/imrn/rnac048</a>","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” <i>International Mathematics Research Notices</i>, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:<a href=\"https://doi.org/10.1093/imrn/rnac048\">10.1093/imrn/rnac048</a>."},"doi":"10.1093/imrn/rnac048","article_processing_charge":"No","day":"01","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","publication":"International Mathematics Research Notices","volume":2023,"date_published":"2023-04-01T00:00:00Z","intvolume":"      2023"},{"title":"Divergence of separated nets with respect to displacement equivalence","oa":1,"article_number":"15","date_created":"2021-07-14T07:01:27Z","citation":{"ista":"Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata., 15.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata (2023).","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” <i>Geometriae Dedicata</i>. Springer Nature, 2023.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>.","apa":"Dymond, M., &#38; Kaluza, V. (2023). Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>, 15, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>."},"arxiv":1,"quality_controlled":"1","doi":"10.1007/s10711-023-00862-3","article_processing_charge":"Yes (via OA deal)","publication":"Geometriae Dedicata","day":"17","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","date_published":"2023-11-17T00:00:00Z","publication_identifier":{"eissn":["1572-9168"],"issn":["0046-5755"]},"isi":1,"month":"11","year":"2023","department":[{"_id":"UlWa"}],"article_type":"original","publisher":"Springer Nature","oa_version":"Published Version","type":"journal_article","publication_status":"epub_ahead","external_id":{"isi":["001105681500001"],"arxiv":["2102.13046"]},"_id":"9651","status":"public","author":[{"full_name":"Dymond, Michael","last_name":"Dymond","first_name":"Michael"},{"first_name":"Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","orcid":"0000-0002-2512-8698","last_name":"Kaluza","full_name":"Kaluza, Vojtech"}],"date_updated":"2024-01-11T13:06:32Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10711-023-00862-3"}],"abstract":[{"lang":"eng","text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence."}],"scopus_import":"1"},{"date_updated":"2023-08-14T11:26:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities.","lang":"eng"}],"keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"scopus_import":"1","author":[{"full_name":"Dymond, Michael","last_name":"Dymond","first_name":"Michael"},{"full_name":"Kaluza, Vojtech","last_name":"Kaluza","orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","first_name":"Vojtech"}],"status":"public","publisher":"Springer Nature","type":"journal_article","oa_version":"Submitted Version","file":[{"date_updated":"2021-07-14T07:41:50Z","content_type":"application/pdf","access_level":"open_access","date_created":"2021-07-14T07:41:50Z","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1","file_size":900422,"file_name":"separated_nets.pdf","relation":"main_file","creator":"vkaluza","file_id":"9653"}],"ddc":["515","516"],"_id":"9652","publication_status":"published","external_id":{"arxiv":["1903.05923"],"isi":["000904950300003"]},"isi":1,"publication_identifier":{"eissn":["1565-8511"]},"month":"03","year":"2023","department":[{"_id":"UlWa"}],"article_type":"original","volume":253,"day":"01","acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","publication":"Israel Journal of Mathematics","has_accepted_license":"1","intvolume":"       253","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s11856-022-2448-6","file_date_updated":"2021-07-14T07:41:50Z","article_processing_charge":"No","oa":1,"citation":{"mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” <i>Israel Journal of Mathematics</i>, vol. 253, Springer Nature, 2023, pp. 501–54, doi:<a href=\"https://doi.org/10.1007/s11856-022-2448-6\">10.1007/s11856-022-2448-6</a>.","apa":"Dymond, M., &#38; Kaluza, V. (2023). Highly irregular separated nets. <i>Israel Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11856-022-2448-6\">https://doi.org/10.1007/s11856-022-2448-6</a>","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” <i>Israel Journal of Mathematics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11856-022-2448-6\">https://doi.org/10.1007/s11856-022-2448-6</a>.","ama":"Dymond M, Kaluza V. Highly irregular separated nets. <i>Israel Journal of Mathematics</i>. 2023;253:501-554. doi:<a href=\"https://doi.org/10.1007/s11856-022-2448-6\">10.1007/s11856-022-2448-6</a>","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” <i>Israel Journal of Mathematics</i>, vol. 253. Springer Nature, pp. 501–554, 2023.","ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554.","short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554."},"date_created":"2021-07-14T07:01:28Z","quality_controlled":"1","arxiv":1,"page":"501-554","title":"Highly irregular separated nets"},{"date_published":"2023-03-01T00:00:00Z","intvolume":"        58","has_accepted_license":"1","publication":"Potential Analysis","day":"01","acknowledgement":"The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper.","volume":58,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"file_date_updated":"2023-10-04T09:18:59Z","doi":"10.1007/s11118-021-09951-y","arxiv":1,"quality_controlled":"1","citation":{"ista":"Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615.","short":"L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.","ieee":"L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” <i>Potential Analysis</i>, vol. 58. Springer Nature, pp. 573–615, 2023.","ama":"Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. <i>Potential Analysis</i>. 2023;58:573-615. doi:<a href=\"https://doi.org/10.1007/s11118-021-09951-y\">10.1007/s11118-021-09951-y</a>","mla":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” <i>Potential Analysis</i>, vol. 58, Springer Nature, 2023, pp. 573–615, doi:<a href=\"https://doi.org/10.1007/s11118-021-09951-y\">10.1007/s11118-021-09951-y</a>.","chicago":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” <i>Potential Analysis</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11118-021-09951-y\">https://doi.org/10.1007/s11118-021-09951-y</a>.","apa":"Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. <i>Potential Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11118-021-09951-y\">https://doi.org/10.1007/s11118-021-09951-y</a>"},"date_created":"2021-10-17T22:01:17Z","oa":1,"title":"Ergodic decomposition of Dirichlet forms via direct integrals and applications","page":"573-615","scopus_import":"1","abstract":[{"text":"We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-04T09:19:12Z","status":"public","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870"}],"external_id":{"arxiv":["2003.01366"],"isi":["000704213400001"]},"publication_status":"published","_id":"10145","type":"journal_article","ddc":["510"],"file":[{"date_created":"2023-10-04T09:18:59Z","success":1,"file_size":806391,"checksum":"625526482be300ca7281c91c30d41725","date_updated":"2023-10-04T09:18:59Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"14387","creator":"dernst","file_name":"2023_PotentialAnalysis_DelloSchiavo.pdf"}],"oa_version":"Published Version","publisher":"Springer Nature","article_type":"original","department":[{"_id":"JaMa"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"year":"2023","month":"03","publication_identifier":{"eissn":["1572-929X"],"issn":["0926-2601"]},"isi":1},{"intvolume":"        11","has_accepted_license":"1","date_published":"2023-09-01T00:00:00Z","volume":11,"day":"01","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s40072-022-00254-w","file_date_updated":"2023-08-14T11:51:04Z","citation":{"mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization  for Correlated Coefficient Fields.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:<a href=\"https://doi.org/10.1007/s40072-022-00254-w\">10.1007/s40072-022-00254-w</a>.","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization  for Correlated Coefficient Fields.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s40072-022-00254-w\">https://doi.org/10.1007/s40072-022-00254-w</a>.","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40072-022-00254-w\">https://doi.org/10.1007/s40072-022-00254-w</a>","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.","ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields,” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, vol. 11. Springer Nature, pp. 1254–1378, 2023.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. 2023;11:1254–1378. doi:<a href=\"https://doi.org/10.1007/s40072-022-00254-w\">10.1007/s40072-022-00254-w</a>"},"date_created":"2021-10-23T10:50:22Z","arxiv":1,"quality_controlled":"1","oa":1,"title":"Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields","page":"1254–1378","abstract":[{"lang":"eng","text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods."}],"scopus_import":"1","date_updated":"2023-08-14T11:51:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas","last_name":"Clozeau","full_name":"Clozeau, Nicolas"}],"status":"public","file":[{"date_created":"2023-08-14T11:51:04Z","file_size":1635193,"checksum":"f83dcaecdbd3ace862c4ed97a20e8501","success":1,"date_updated":"2023-08-14T11:51:04Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"14052","creator":"dernst","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf"}],"type":"journal_article","oa_version":"Published Version","ddc":["510"],"_id":"10173","publication_status":"published","external_id":{"arxiv":["2102.07452"],"isi":["000799715600001"]},"publisher":"Springer Nature","department":[{"_id":"JuFi"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["2194-0401"]},"month":"09","year":"2023"},{"publisher":"Wiley","_id":"10405","issue":"5","publication_status":"published","external_id":{"arxiv":["1912.04100"],"isi":["000724652500001"]},"type":"journal_article","ddc":["510"],"file":[{"date_updated":"2023-10-04T09:21:48Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-10-04T09:21:48Z","file_size":803440,"success":1,"checksum":"8346bc2642afb4ccb7f38979f41df5d9","file_name":"2023_CommPureMathematics_Cipolloni.pdf","relation":"main_file","file_id":"14388","creator":"dernst"}],"oa_version":"Published Version","year":"2023","month":"05","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication_identifier":{"eissn":["1097-0312"],"issn":["0010-3640"]},"article_type":"original","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-04T09:22:55Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. "}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"status":"public","oa":1,"arxiv":1,"quality_controlled":"1","date_created":"2021-12-05T23:01:41Z","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” <i>Communications on Pure and Applied Mathematics</i>, vol. 76, no. 5. Wiley, pp. 946–1034, 2023.","ama":"Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. <i>Communications on Pure and Applied Mathematics</i>. 2023;76(5):946-1034. doi:<a href=\"https://doi.org/10.1002/cpa.22028\">10.1002/cpa.22028</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/cpa.22028\">https://doi.org/10.1002/cpa.22028</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.22028\">https://doi.org/10.1002/cpa.22028</a>","mla":"Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” <i>Communications on Pure and Applied Mathematics</i>, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:<a href=\"https://doi.org/10.1002/cpa.22028\">10.1002/cpa.22028</a>."},"page":"946-1034","title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","volume":76,"acknowledgement":"L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","day":"01","publication":"Communications on Pure and Applied Mathematics","date_published":"2023-05-01T00:00:00Z","has_accepted_license":"1","intvolume":"        76","file_date_updated":"2023-10-04T09:21:48Z","doi":"10.1002/cpa.22028","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"}},{"date_updated":"2023-08-01T14:40:33Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"full_name":"Fellner, Klemens","last_name":"Fellner","first_name":"Klemens"},{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L"},{"first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333"},{"full_name":"Tang, Bao Quoc","last_name":"Tang","first_name":"Bao Quoc"}],"publisher":"Springer Nature","oa_version":"Published Version","type":"journal_article","ddc":["510"],"file":[{"date_updated":"2023-06-19T07:33:53Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-06-19T07:33:53Z","success":1,"checksum":"f3f0f0886098e31c81116cff8183750b","file_size":742315,"file_name":"2023_JourNonlinearScience_Fellner.pdf","relation":"main_file","creator":"dernst","file_id":"13149"}],"external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"publication_status":"published","_id":"10550","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"isi":1,"year":"2023","month":"06","department":[{"_id":"JuFi"}],"article_type":"original","day":"07","publication":"Journal of Nonlinear Science","acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","volume":33,"intvolume":"        33","has_accepted_license":"1","date_published":"2023-06-07T00:00:00Z","doi":"10.1007/s00332-023-09926-w","file_date_updated":"2023-06-19T07:33:53Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","oa":1,"article_number":"66","citation":{"mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” <i>Journal of Nonlinear Science</i>, vol. 33, 66, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00332-023-09926-w\">10.1007/s00332-023-09926-w</a>.","apa":"Fellner, K., Fischer, J. L., Kniely, M., &#38; Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. <i>Journal of Nonlinear Science</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00332-023-09926-w\">https://doi.org/10.1007/s00332-023-09926-w</a>","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” <i>Journal of Nonlinear Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00332-023-09926-w\">https://doi.org/10.1007/s00332-023-09926-w</a>.","ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. <i>Journal of Nonlinear Science</i>. 2023;33. doi:<a href=\"https://doi.org/10.1007/s00332-023-09926-w\">10.1007/s00332-023-09926-w</a>","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” <i>Journal of Nonlinear Science</i>, vol. 33. Springer Nature, 2023."},"date_created":"2021-12-16T12:15:35Z","arxiv":1,"quality_controlled":"1","title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion"},{"abstract":[{"text":"The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1  (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles.","lang":"eng"}],"scopus_import":"1","date_updated":"2024-01-30T12:10:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","full_name":"Cornalba, Federico","last_name":"Cornalba","orcid":"0000-0002-6269-5149"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"}],"ddc":["510"],"file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2024-01-30T12:09:34Z","checksum":"4529eeff170b6745a461d397ee611b5a","file_size":1851185,"success":1,"date_created":"2024-01-30T12:09:34Z","file_name":"2023_ArchiveRationalMech_Cornalba.pdf","creator":"dernst","file_id":"14904","relation":"main_file"}],"type":"journal_article","oa_version":"Published Version","external_id":{"arxiv":["2109.06500"],"isi":["001043086800001"]},"publication_status":"published","issue":"5","_id":"10551","publisher":"Springer Nature","department":[{"_id":"JuFi"}],"article_type":"original","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"year":"2023","month":"08","has_accepted_license":"1","intvolume":"       247","date_published":"2023-08-04T00:00:00Z","day":"04","acknowledgement":"We thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science Fund (FWF).","publication":"Archive for Rational Mechanics and Analysis","volume":247,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00205-023-01903-7","file_date_updated":"2024-01-30T12:09:34Z","citation":{"short":"F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247 (2023).","ieee":"F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 5. Springer Nature, 2023.","ista":"Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 247(5), 76.","ama":"Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. <i>Archive for Rational Mechanics and Analysis</i>. 2023;247(5). doi:<a href=\"https://doi.org/10.1007/s00205-023-01903-7\">10.1007/s00205-023-01903-7</a>","chicago":"Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00205-023-01903-7\">https://doi.org/10.1007/s00205-023-01903-7</a>.","apa":"Cornalba, F., &#38; Fischer, J. L. (2023). The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-023-01903-7\">https://doi.org/10.1007/s00205-023-01903-7</a>","mla":"Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 5, 76, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00205-023-01903-7\">10.1007/s00205-023-01903-7</a>."},"date_created":"2021-12-16T12:16:03Z","quality_controlled":"1","arxiv":1,"oa":1,"article_number":"76","title":"The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles"},{"title":"Inserting one edge into a simple drawing is hard","page":"745–770","date_created":"2022-08-28T22:02:01Z","citation":{"apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., &#38; Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>","chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00394-9\">https://doi.org/10.1007/s00454-022-00394-9</a>.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” <i>Discrete and Computational Geometry</i>, vol. 69, Springer Nature, 2023, pp. 745–770, doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. <i>Discrete and Computational Geometry</i>. 2023;69:745–770. doi:<a href=\"https://doi.org/10.1007/s00454-022-00394-9\">10.1007/s00454-022-00394-9</a>","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” <i>Discrete and Computational Geometry</i>, vol. 69. Springer Nature, pp. 745–770, 2023."},"arxiv":1,"quality_controlled":"1","oa":1,"article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00454-022-00394-9","file_date_updated":"2022-08-29T11:23:15Z","has_accepted_license":"1","intvolume":"        69","date_published":"2023-04-01T00:00:00Z","volume":69,"acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","day":"01","publication":"Discrete and Computational Geometry","department":[{"_id":"UlWa"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"year":"2023","month":"04","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"oa_version":"Published Version","type":"journal_article","ddc":["510"],"file":[{"file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","file_id":"12006","creator":"alisjak","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-08-29T11:23:15Z","success":1,"file_size":1002218,"checksum":"def7ae3b28d9fd6aec16450e40090302","date_created":"2022-08-29T11:23:15Z"}],"_id":"11999","publication_status":"published","external_id":{"isi":["000840292800001"],"arxiv":["1909.07347"]},"publisher":"Springer Nature","author":[{"last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M"},{"full_name":"Klute, Fabian","last_name":"Klute","first_name":"Fabian"},{"last_name":"Parada","full_name":"Parada, Irene","first_name":"Irene"},{"first_name":"Birgit","last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit"},{"full_name":"Seidel, Raimund","last_name":"Seidel","first_name":"Raimund"},{"last_name":"Wiedera","full_name":"Wiedera, Tilo","first_name":"Tilo"}],"status":"public","abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-14T12:51:25Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_type":"original","department":[{"_id":"HeEd"}],"year":"2023","month":"01","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"isi":1,"publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"_id":"12086","external_id":{"isi":["000846967100001"]},"publication_status":"published","type":"journal_article","file":[{"relation":"main_file","file_id":"12322","creator":"dernst","file_name":"2023_Algorithmica_Edelsbrunner.pdf","date_created":"2023-01-20T10:02:48Z","success":1,"checksum":"71685ca5121f4c837f40c3f8eb50c915","file_size":911017,"date_updated":"2023-01-20T10:02:48Z","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["510"],"publisher":"Springer Nature","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Osang","full_name":"Osang, Georg F","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"status":"public","scopus_import":"1","abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-06-27T12:53:43Z","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","page":"277-295","quality_controlled":"1","date_created":"2022-09-11T22:01:57Z","citation":{"ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. 2023;85:277-295. doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 277–295, 2023.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-022-01027-6\">https://doi.org/10.1007/s00453-022-01027-6</a>.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 277–95, doi:<a href=\"https://doi.org/10.1007/s00453-022-01027-6\">10.1007/s00453-022-01027-6</a>."},"oa":1,"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-01-20T10:02:48Z","doi":"10.1007/s00453-022-01027-6","date_published":"2023-01-01T00:00:00Z","has_accepted_license":"1","intvolume":"        85","volume":85,"day":"01","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","publication":"Algorithmica"},{"publication":"Annales Henri Poincare","acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","day":"01","volume":24,"has_accepted_license":"1","intvolume":"        24","date_published":"2023-03-01T00:00:00Z","doi":"10.1007/s00023-022-01220-x","file_date_updated":"2023-08-14T11:38:28Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"oa":1,"citation":{"ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. 2023;24:717-750. doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>","ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” <i>Annales Henri Poincare</i>, vol. 24. Springer Nature, pp. 717–750, 2023.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","apa":"Wirth, M., &#38; Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-022-01220-x\">https://doi.org/10.1007/s00023-022-01220-x</a>.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” <i>Annales Henri Poincare</i>, vol. 24, Springer Nature, 2023, pp. 717–50, doi:<a href=\"https://doi.org/10.1007/s00023-022-01220-x\">10.1007/s00023-022-01220-x</a>."},"date_created":"2022-09-11T22:01:57Z","arxiv":1,"quality_controlled":"1","page":"717-750","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","date_updated":"2023-08-14T11:39:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","full_name":"Zhang, Haonan","last_name":"Zhang"}],"publisher":"Springer Nature","type":"journal_article","ddc":["510"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14051","creator":"dernst","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","date_created":"2023-08-14T11:38:28Z","checksum":"8c7b185eba5ccd92ef55c120f654222c","file_size":554871,"success":1,"date_updated":"2023-08-14T11:38:28Z","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","external_id":{"isi":["000837499800002"],"arxiv":["2105.08303"]},"_id":"12087","publication_identifier":{"issn":["1424-0637"]},"isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"M03337","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis"},{"grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"year":"2023","month":"03","department":[{"_id":"JaMa"}],"article_type":"original"},{"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","citation":{"ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. 2023;23(1). doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” <i>Journal of Evolution Equations</i>, vol. 23, no. 1. Springer Nature, 2023.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","apa":"Dello Schiavo, L., &#38; Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. <i>Journal of Evolution Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00028-022-00859-7\">https://doi.org/10.1007/s00028-022-00859-7</a>.","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” <i>Journal of Evolution Equations</i>, vol. 23, no. 1, 9, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00028-022-00859-7\">10.1007/s00028-022-00859-7</a>."},"date_created":"2023-01-08T23:00:53Z","quality_controlled":"1","article_number":"9","oa":1,"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00028-022-00859-7","file_date_updated":"2023-01-20T10:45:06Z","intvolume":"        23","has_accepted_license":"1","date_published":"2023-01-01T00:00:00Z","volume":23,"publication":"Journal of Evolution Equations","day":"01","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","department":[{"_id":"JaMa"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"month":"01","year":"2023","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"},{"grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","name":"Configuration Spaces over Non-Smooth Spaces"},{"_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N"}],"file":[{"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","relation":"main_file","creator":"dernst","file_id":"12325","date_updated":"2023-01-20T10:45:06Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-20T10:45:06Z","success":1,"file_size":422612,"checksum":"1f34f3e2cb521033de6154f274ea3a4e"}],"ddc":["510"],"type":"journal_article","oa_version":"Published Version","_id":"12104","issue":"1","external_id":{"isi":["000906214600004"]},"publication_status":"published","publisher":"Springer Nature","author":[{"first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241"}],"status":"public","abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-06-28T11:54:35Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.1017/jfm.2022.1001","file_date_updated":"2023-02-02T12:34:54Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","day":"10","publication":"Journal of Fluid Mechanics","volume":954,"intvolume":"       954","has_accepted_license":"1","date_published":"2023-01-10T00:00:00Z","title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","oa":1,"article_number":"A10","citation":{"chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/jfm.2022.1001\">https://doi.org/10.1017/jfm.2022.1001</a>.","apa":"Marensi, E., Yalniz, G., Hof, B., &#38; Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2022.1001\">https://doi.org/10.1017/jfm.2022.1001</a>","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” <i>Journal of Fluid Mechanics</i>, vol. 954, A10, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/jfm.2022.1001\">10.1017/jfm.2022.1001</a>.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” <i>Journal of Fluid Mechanics</i>, vol. 954. Cambridge University Press, 2023.","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. <i>Journal of Fluid Mechanics</i>. 2023;954. doi:<a href=\"https://doi.org/10.1017/jfm.2022.1001\">10.1017/jfm.2022.1001</a>"},"date_created":"2023-01-08T23:00:53Z","arxiv":1,"quality_controlled":"1","status":"public","author":[{"first_name":"Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","full_name":"Marensi, Elena"},{"first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","last_name":"Yalniz","full_name":"Yalniz, Gökhan"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"},{"orcid":"0000-0003-0423-5010","last_name":"Budanur","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-01T12:53:23Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"isi":1,"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"month":"01","year":"2023","department":[{"_id":"BjHo"}],"article_type":"original","publisher":"Cambridge University Press","file":[{"file_id":"12489","creator":"dernst","relation":"main_file","file_name":"2023_JourFluidMechanics_Marensi.pdf","checksum":"9224f987caefe5dd85a70814d3cce65c","success":1,"file_size":1931647,"date_created":"2023-02-02T12:34:54Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-02-02T12:34:54Z"}],"type":"journal_article","ddc":["530"],"oa_version":"Published Version","external_id":{"isi":["000903336600001"],"arxiv":["2101.07516"]},"publication_status":"published","_id":"12105"},{"type":"journal_article","oa_version":"None","publication_status":"epub_ahead","external_id":{"isi":["000911497000001"]},"_id":"12113","publisher":"Elsevier","department":[{"_id":"MaIb"}],"article_type":"original","publication_identifier":{"issn":["0169-4332"]},"isi":1,"year":"2023","month":"03","keyword":["Surfaces","Coatings and Films","Condensed Matter Physics","Surfaces and Interfaces","General Physics and Astronomy","General Chemistry"],"abstract":[{"lang":"eng","text":"The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices."}],"scopus_import":"1","date_updated":"2023-08-14T11:47:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","author":[{"last_name":"Zhang","full_name":"Zhang, Li","first_name":"Li"},{"last_name":"Liu","full_name":"Liu, Xingyu","first_name":"Xingyu"},{"first_name":"Ting","last_name":"Wu","full_name":"Wu, Ting"},{"first_name":"Shengduo","id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","full_name":"Xu, Shengduo","last_name":"Xu"},{"first_name":"Guoquan","last_name":"Suo","full_name":"Suo, Guoquan"},{"first_name":"Xiaohui","last_name":"Ye","full_name":"Ye, Xiaohui"},{"first_name":"Xiaojiang","full_name":"Hou, Xiaojiang","last_name":"Hou"},{"full_name":"Yang, Yanling","last_name":"Yang","first_name":"Yanling"},{"first_name":"Qingfeng","full_name":"Liu, Qingfeng","last_name":"Liu"},{"first_name":"Hongqiang","full_name":"Wang, Hongqiang","last_name":"Wang"}],"date_created":"2023-01-12T11:55:02Z","citation":{"chicago":"Zhang, Li, Xingyu Liu, Ting Wu, Shengduo Xu, Guoquan Suo, Xiaohui Ye, Xiaojiang Hou, Yanling Yang, Qingfeng Liu, and Hongqiang Wang. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” <i>Applied Surface Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">https://doi.org/10.1016/j.apsusc.2022.156101</a>.","apa":"Zhang, L., Liu, X., Wu, T., Xu, S., Suo, G., Ye, X., … Wang, H. (2023). Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. <i>Applied Surface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">https://doi.org/10.1016/j.apsusc.2022.156101</a>","mla":"Zhang, Li, et al. “Two-Step Post-Treatment to Deliver High Performance Thermoelectric Device with Vertical Temperature Gradient.” <i>Applied Surface Science</i>, vol. 613, 156101, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">10.1016/j.apsusc.2022.156101</a>.","short":"L. Zhang, X. Liu, T. Wu, S. Xu, G. Suo, X. Ye, X. Hou, Y. Yang, Q. Liu, H. Wang, Applied Surface Science 613 (2023).","ista":"Zhang L, Liu X, Wu T, Xu S, Suo G, Ye X, Hou X, Yang Y, Liu Q, Wang H. 2023. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. Applied Surface Science. 613, 156101.","ieee":"L. Zhang <i>et al.</i>, “Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient,” <i>Applied Surface Science</i>, vol. 613. Elsevier, 2023.","ama":"Zhang L, Liu X, Wu T, et al. Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient. <i>Applied Surface Science</i>. 2023;613. doi:<a href=\"https://doi.org/10.1016/j.apsusc.2022.156101\">10.1016/j.apsusc.2022.156101</a>"},"quality_controlled":"1","article_number":"156101","title":"Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient","intvolume":"       613","date_published":"2023-03-15T00:00:00Z","acknowledgement":"Scientific Research Program Funded by Shaanxi Provincial Education Department (Program No.22JY012), Natural Science Basic Research Program of Shaanxi (Grant No.2022JZ-31), Young Talent fund of University Association for Science and Technology in Shaanxi, China (Grant No.20210411), China Postdoctoral Science Foundation (Grant No. 2021M692621), the Foundation of Shaanxi University of Science & Technology (Grant No. 2017GBJ-03), Open Foundation of Key Laboratory of Auxiliary Chemistry and Technology for Chemical Industry, Ministry of Education, Shaanxi University of Science and Technology (Grant No. KFKT2022-15), and Open Foundation of Shaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and Technology, Shaanxi University of Science and Technology (Grant No. KFKT2022-15).","publication":"Applied Surface Science","day":"15","volume":613,"article_processing_charge":"No","doi":"10.1016/j.apsusc.2022.156101"},{"acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","day":"01","publication":"Journal of Structural Biology: X","volume":7,"pmid":1,"has_accepted_license":"1","intvolume":"         7","date_published":"2023-01-01T00:00:00Z","doi":"10.1016/j.yjsbx.2022.100079","file_date_updated":"2023-08-16T09:36:28Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"article_processing_charge":"No","oa":1,"article_number":"100079","date_created":"2023-01-12T11:55:38Z","citation":{"ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” <i>Journal of Structural Biology: X</i>, vol. 7. Elsevier, 2023.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. 2023;7. doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., &#38; Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. <i>Journal of Structural Biology: X</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">https://doi.org/10.1016/j.yjsbx.2022.100079</a>","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” <i>Journal of Structural Biology: X</i>, vol. 7, 100079, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.yjsbx.2022.100079\">10.1016/j.yjsbx.2022.100079</a>."},"quality_controlled":"1","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","date_updated":"2023-08-16T09:37:25Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Structural Biology"],"abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"full_name":"Lebedenko, Olga O.","last_name":"Lebedenko","first_name":"Olga O."},{"last_name":"Becker","full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"first_name":"Isabel","full_name":"Ayala, Isabel","last_name":"Ayala"},{"last_name":"Lichtenecker","full_name":"Lichtenecker, Roman","first_name":"Roman"},{"first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R.","last_name":"Skrynnikov"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"publisher":"Elsevier","oa_version":"Published Version","type":"journal_article","ddc":["570"],"file":[{"date_created":"2023-08-16T09:36:28Z","file_size":5132322,"success":1,"checksum":"b4b1c10a31018aafe053b7d55a470e54","date_updated":"2023-08-16T09:36:28Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"14064","creator":"dernst","file_name":"2023_JourStrucBiologyX_Gauto.pdf"}],"publication_status":"published","external_id":{"pmid":["36578472"]},"_id":"12114","publication_identifier":{"issn":["2590-1524"]},"month":"01","year":"2023","department":[{"_id":"PaSc"}],"article_type":"original"}]