[{"date_updated":"2026-06-19T22:31:16Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Superconductivity from a melted insulator in Josephson junction arrays","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"ec_funded":1,"_id":"14032","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"isi":1,"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"type":"journal_article","publication_status":"published","publisher":"Springer Nature","oa_version":"Published Version","project":[{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"month":"11","article_type":"original","keyword":["General Physics and Astronomy"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","ddc":["530"],"abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"file_date_updated":"2024-01-29T11:25:38Z","oa":1,"intvolume":"        19","related_material":{"record":[{"id":"17881","relation":"dissertation_contains","status":"public"}]},"doi":"10.1038/s41567-023-02161-w","scopus_import":"1","citation":{"mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>.","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023."},"quality_controlled":"1","date_created":"2023-08-11T07:41:17Z","day":"01","corr_author":"1","year":"2023","publication":"Nature Physics","page":"1630-1635","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":1977706,"file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","date_created":"2024-01-29T11:25:38Z","checksum":"1fc86d71bfbf836e221c1e925343adc5","date_updated":"2024-01-29T11:25:38Z","relation":"main_file","creator":"dernst","file_id":"14899"}],"date_published":"2023-11-01T00:00:00Z","external_id":{"isi":["001054563800006"]},"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","first_name":"Soham"},{"first_name":"Jorden L","orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior"},{"full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo","first_name":"Jaime"},{"first_name":"Denise","orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","first_name":"Martin"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"}],"volume":19,"acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","status":"public"},{"article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"abstract":[{"text":"During my Ph.D. research, I managed a series of projects, each focused on the\r\nmechanisms underlying cell migration. My work involved an in-depth examination of\r\nthe complex strategies employed by neutrophils, with a specific focus on their ability to\r\nsynchronize spatial-temporal cues and optimize their gradient perception. However, it\r\nis essential to acknowledge that not all projects yielded successful results, as some\r\nideas were discontinued and are archived for future reference within this thesis.\r\nMy main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source\r\ntype – linear or point-like. By combining single-cell tracking in 3D environments with\r\nproxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger\r\nresponse to semi-exponential gradients from point sources. In addition, neutrophils\r\nexhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over\r\ntime and employed a \"Run and Fumble\" strategy, alternating between consistent runs\r\nand strategic \"tumbles\" for efficient navigation.\r\nThe project extended to the possibility of cells amplifying perceived gradients by\r\nenclosing their immediate surroundings, pushing attractants forward for enrichment\r\nwhile depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences\r\nin migratory efficacy were detected across pore sizes and device heights, quantifying\r\ngradient manipulation effects proved challenging.\r\nThe \"Laser-Assisted Protein Adsorption by Photobleaching\" (LAPAP) project was\r\npromising, as it allowed the printing of gradients. Initially successful with dendritic cells,\r\nwe aimed to adapt it for neutrophils. Through extensive experimentation with multiple\r\nparameters, we attempted to trigger responses from neutrophils. Despite these efforts\r\nand collaboration, the project failed due to practical challenges and limitations.\r\nFacing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8\r\nprimary murine cell line. Despite their existence, their migratory behavior was largely\r\nunexplored due to potential limitations. Through differentiation protocol refinements we\r\nenhanced their migratory capabilities, though their capacity still lagged behind human\r\nneutrophils. Despite this, the improved migration potential of these cells pointed toward\r\ntheir utility for in vitro murine neutrophil migration studies.","lang":"eng"}],"oa":1,"file_date_updated":"2024-12-20T23:30:04Z","related_material":{"record":[{"id":"14360","status":"public","relation":"part_of_dissertation"},{"id":"12272","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6328"},{"status":"public","relation":"part_of_dissertation","id":"7885"},{"status":"public","relation":"part_of_dissertation","id":"14274"}]},"doi":"10.15479/at:ista:14697","date_created":"2023-12-18T19:14:28Z","citation":{"ama":"Stopp JA. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","short":"J.A. Stopp, Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","ieee":"J. A. Stopp, “Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>","chicago":"Stopp, Julian A. “Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","mla":"Stopp, Julian A. <i>Neutrophils on the Hunt : Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","ista":"Stopp JA. 2023. Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria."},"corr_author":"1","day":"20","alternative_title":["ISTA Thesis"],"year":"2023","language":[{"iso":"eng"}],"page":"226","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"checksum":"457927165d5d556305d3086f6b83e5c7","date_created":"2023-12-20T09:35:34Z","content_type":"application/pdf","access_level":"open_access","file_name":"Thesis.pdf","file_size":51585778,"file_id":"14699","creator":"jstopp","embargo":"2024-12-20","relation":"main_file","date_updated":"2024-12-20T23:30:04Z"},{"date_updated":"2024-12-20T23:30:04Z","creator":"jstopp","embargo_to":"open_access","file_id":"14700","relation":"source_file","file_name":"Thesis.docx","file_size":69625950,"checksum":"e8d26449ac461f5e8478a62c9507506f","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-12-20T09:35:35Z"}],"date_published":"2023-12-20T00:00:00Z","author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A"}],"status":"public","date_updated":"2026-06-18T17:34:48Z","title":"Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"_id":"14697","ec_funded":1,"OA_place":"publisher","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663-337X"]},"publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","degree_awarded":"PhD","month":"12","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"}]},{"status":"public","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.","date_published":"2023-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jonna H","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko"},{"last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217","first_name":"Mehmet C"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","full_name":"Canigova, Nikola","orcid":"0000-0002-8518-5926"},{"last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","first_name":"Julian A"},{"first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"volume":8,"language":[{"iso":"eng"}],"publication":"Science Immunology","issue":"87","year":"2023","scopus_import":"1","citation":{"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>","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>.","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>","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)."},"quality_controlled":"1","date_created":"2023-09-06T08:07:51Z","corr_author":"1","day":"01","intvolume":"         8","related_material":{"record":[{"id":"14279","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"19745"},{"id":"14697","relation":"dissertation_contains","status":"public"}]},"doi":"10.1126/sciimmunol.adc9584","abstract":[{"lang":"eng","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."}],"ddc":["570"],"oa":1,"article_processing_charge":"No","article_number":"adc9584","keyword":["General Medicine","Immunology"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"09","article_type":"original","publisher":"American Association for the Advancement of Science","type":"journal_article","publication_status":"published","oa_version":"Published Version","isi":1,"publication_identifier":{"issn":["2470-9468"]},"ec_funded":1,"_id":"14274","pmid":1,"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","date_updated":"2026-06-19T22:31:20Z"},{"type":"journal_article","publication_status":"published","publisher":"Springer Nature","oa_version":"Published Version","month":"09","article_type":"original","date_updated":"2026-06-19T22:31:20Z","department":[{"_id":"MiSi"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","_id":"14360","pmid":1,"isi":1,"publication_identifier":{"eissn":["2041-1723"]},"year":"2023","language":[{"iso":"eng"}],"publication":"Nature Communications","file":[{"file_id":"14365","creator":"dernst","relation":"main_file","date_updated":"2023-09-25T08:22:58Z","checksum":"ad670e3b3c64fc585675948370f6b149","date_created":"2023-09-25T08:22:58Z","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureComm_Sitarska.pdf","success":1,"file_size":2725421}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-09-13T00:00:00Z","author":[{"first_name":"Ewa","last_name":"Sitarska","full_name":"Sitarska, Ewa"},{"first_name":"Silvia Dias","full_name":"Almeida, Silvia Dias","last_name":"Almeida"},{"last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold","first_name":"Marianne Sandvold"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"last_name":"Czuchnowski","full_name":"Czuchnowski, Jakub","first_name":"Jakub"},{"full_name":"Siggel, Marc","last_name":"Siggel","first_name":"Marc"},{"full_name":"Roessner, Rita","last_name":"Roessner","first_name":"Rita"},{"first_name":"Aline","full_name":"Tschanz, Aline","last_name":"Tschanz"},{"full_name":"Ejsing, Christer","last_name":"Ejsing","first_name":"Christer"},{"full_name":"Schwab, Yannick","last_name":"Schwab","first_name":"Yannick"},{"full_name":"Kosinski, Jan","last_name":"Kosinski","first_name":"Jan"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Anna","last_name":"Kreshuk","full_name":"Kreshuk, Anna"},{"last_name":"Erzberger","full_name":"Erzberger, Anna","first_name":"Anna"},{"last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba","first_name":"Alba"}],"external_id":{"isi":["001087583700008"],"pmid":["37704612"]},"volume":14,"status":"public","acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","article_processing_charge":"Yes (via OA deal)","article_number":"5644","has_accepted_license":"1","ddc":["570"],"abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"file_date_updated":"2023-09-25T08:22:58Z","oa":1,"intvolume":"        14","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"}]},"doi":"10.1038/s41467-023-41173-1","scopus_import":"1","date_created":"2023-09-24T22:01:10Z","citation":{"short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644."},"quality_controlled":"1","day":"13"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.13468","open_access":"1"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"month":"07","arxiv":1,"oa_version":"Preprint","type":"conference","publication_status":"published","publisher":"ML Research Press","publication_identifier":{"eissn":["2640-3498"]},"_id":"14459","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"date_updated":"2026-06-19T22:31:21Z","status":"public","acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","volume":202,"external_id":{"arxiv":["2212.13468"]},"author":[{"first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko"},{"first_name":"Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","last_name":"Kögler","full_name":"Kögler, Kevin"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco"}],"date_published":"2023-07-30T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 40th International Conference on Machine Learning","page":"31151-31209","language":[{"iso":"eng"}],"year":"2023","day":"30","corr_author":"1","alternative_title":["PMLR"],"citation":{"ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:31151-31209.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:31151–209. ML Research Press, 2023.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 31151–209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., &#38; Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press."},"quality_controlled":"1","date_created":"2023-10-29T23:01:17Z","scopus_import":"1","related_material":{"record":[{"id":"17465","relation":"dissertation_contains","status":"public"}]},"intvolume":"       202","oa":1,"abstract":[{"lang":"eng","text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions."}],"conference":{"name":"ICML: International Conference on Machine Learning","location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29","start_date":"2023-07-23"},"article_processing_charge":"No"},{"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","ec_funded":1,"_id":"14422","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"title":"Synapseek: Meta-learning synaptic plasticity rules","department":[{"_id":"GradSch"},{"_id":"TiVo"}],"date_updated":"2026-06-18T19:55:49Z","supervisor":[{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"}],"project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"month":"10","degree_awarded":"PhD","oa_version":"Published Version","publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"day":"12","corr_author":"1","citation":{"ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>.","apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023."},"date_created":"2023-10-12T14:13:25Z","doi":"10.15479/at:ista:14422","related_material":{"record":[{"id":"9633","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2024-10-13T22:30:04Z","oa":1,"ddc":["610"],"abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","status":"public","author":[{"full_name":"Confavreux, Basile J","last_name":"Confavreux","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2023-10-12T00:00:00Z","file":[{"date_updated":"2024-10-13T22:30:04Z","relation":"main_file","embargo":"2024-10-12","file_id":"14424","creator":"cchlebak","file_size":30599717,"file_name":"Confavreux_Thesis_2A.pdf","date_created":"2023-10-12T14:53:50Z","content_type":"application/pdf","access_level":"open_access","checksum":"7f636555eae7803323df287672fd13ed"},{"date_updated":"2024-10-13T22:30:04Z","embargo_to":"open_access","creator":"cchlebak","file_id":"14440","relation":"source_file","file_name":"Confavreux Thesis.zip","file_size":68406739,"checksum":"725e85946db92290a4583a0de9779e1b","content_type":"application/x-zip-compressed","access_level":"closed","date_created":"2023-10-18T07:38:34Z"}],"page":"148","language":[{"iso":"eng"}],"year":"2023"},{"abstract":[{"text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. ","lang":"eng"}],"ddc":["000"],"oa":1,"file_date_updated":"2022-06-28T08:32:58Z","article_number":"112","article_processing_charge":"No","has_accepted_license":"1","citation":{"ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022.","ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>","mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>.","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>."},"quality_controlled":"1","date_created":"2022-06-10T06:41:47Z","scopus_import":"1","day":"01","corr_author":"1","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/","relation":"press_release"}]},"intvolume":"        41","doi":"10.1145/3528223.3530144","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","issue":"4","year":"2022","acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","status":"public","date_published":"2022-06-01T00:00:00Z","file":[{"date_updated":"2022-06-28T08:32:58Z","creator":"dernst","file_id":"11467","relation":"main_file","success":1,"file_name":"2022_ACM_acceptedversion_Piovarci.pdf","file_size":33994829,"checksum":"27f6fe41c6ff84d50445cc9b0176d45b","access_level":"open_access","content_type":"application/pdf","date_created":"2022-06-28T08:32:58Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":41,"author":[{"first_name":"Michael","full_name":"Piovarci, Michael","orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci"},{"first_name":"Michael","full_name":"Foshey, Michael","last_name":"Foshey"},{"first_name":"Jie","last_name":"Xu","full_name":"Xu, Jie"},{"first_name":"Timothy","last_name":"Erps","full_name":"Erps, Timothy"},{"first_name":"Vahid","last_name":"Babaei","full_name":"Babaei, Vahid"},{"first_name":"Piotr","last_name":"Didyk","full_name":"Didyk, Piotr"},{"last_name":"Rusinkiewicz","full_name":"Rusinkiewicz, Szymon","first_name":"Szymon"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"external_id":{"arxiv":["2201.11819"],"isi":["000830989200091"]},"department":[{"_id":"BeBi"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Closed-loop control of direct ink writing via reinforcement learning","date_updated":"2025-09-10T09:36:45Z","OA_place":"publisher","isi":1,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"_id":"11442","ec_funded":1,"arxiv":1,"publication_status":"published","type":"journal_article","publisher":"Association for Computing Machinery","oa_version":"Submitted Version","OA_type":"hybrid","PlanS_conform":"1","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"},{"grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"month":"06","article_type":"original"},{"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2006.08836","open_access":"1"}],"month":"06","article_type":"original","arxiv":1,"publisher":"American Mathematical Society","type":"journal_article","publication_status":"published","oa_version":"Preprint","isi":1,"publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"_id":"11443","department":[{"_id":"MaKw"}],"title":"Extension complexity of low-dimensional polytopes","date_updated":"2024-10-09T21:02:31Z","acknowledgement":"The research of the first author was supported by SNSF Project 178493 and NSF Award DMS-1953990. The research of the second author supported by NSF Award DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176, NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum Fund. ","status":"public","date_published":"2022-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":375,"author":[{"first_name":"Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan"},{"first_name":"Lisa","full_name":"Sauermann, Lisa","last_name":"Sauermann"},{"first_name":"Yufei","full_name":"Zhao, Yufei","last_name":"Zhao"}],"external_id":{"isi":["000798461500001"],"arxiv":["2006.08836"]},"page":"4209-4250","language":[{"iso":"eng"}],"publication":"Transactions of the American Mathematical Society","issue":"6","year":"2022","quality_controlled":"1","date_created":"2022-06-12T22:01:45Z","citation":{"mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>.","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>","chicago":"Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2022. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>.","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","ama":"Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. 2022;375(6):4209-4250. doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250.","ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022."},"scopus_import":"1","day":"01","corr_author":"1","intvolume":"       375","doi":"10.1090/tran/8614","abstract":[{"lang":"eng","text":"Sometimes, it is possible to represent a complicated polytope as a projection of a much simpler polytope. To quantify this phenomenon, the extension complexity of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional) polytope from which P can be obtained as a (linear) projection. This notion is motivated by its relevance to combinatorial optimisation, and has been studied intensively for various specific polytopes associated with important optimisation problems. In this paper we study extension complexity as a parameter of general polytopes, more specifically considering various families of low-dimensional polytopes. First, we prove that for a fixed dimension d, the extension complexity of a random d-dimensional polytope (obtained as the convex hull of random points in a ball or on a sphere) is typically on the order of the square root of its number of vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie on a circle) has extension complexity at most 24√n. This bound is tight up to the constant factor 24. Finally, we show that there exists an no(1)-dimensional polytope with at most n vertices and extension complexity n1−o(1). Our theorems are proved with a range of different techniques, which we hope will be of further interest."}],"oa":1,"article_processing_charge":"No"},{"page":"23-41","publication":"Library and Information History","language":[{"iso":"eng"}],"issue":"1","year":"2022","status":"public","date_published":"2022-04-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Clara A","last_name":"Chlebak","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","full_name":"Chlebak, Clara A","orcid":"0000-0002-3385-3865"},{"first_name":"Peter H.","last_name":"Reid","full_name":"Reid, Peter H."}],"volume":38,"abstract":[{"lang":"eng","text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride."}],"oa":1,"article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","citation":{"short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>.","apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>"},"date_created":"2022-06-12T22:01:45Z","day":"01","corr_author":"1","intvolume":"        38","doi":"10.3366/lih.2022.0097","publication_status":"published","type":"journal_article","publisher":"Edinburgh University Press","oa_version":"Submitted Version","main_file_link":[{"url":"https://rgu-repository.worktribe.com/output/1635939","open_access":"1"}],"month":"04","article_type":"original","department":[{"_id":"E-Lib"}],"title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","date_updated":"2024-10-09T21:02:31Z","publication_identifier":{"issn":["1758-3489"],"eissn":["1758-3497"]},"_id":"11444"},{"year":"2022","language":[{"iso":"eng"}],"publication":"Angewandte Chemie - International Edition","issue":"31","file":[{"date_updated":"2022-07-29T09:29:20Z","creator":"dernst","file_id":"11696","relation":"main_file","success":1,"file_name":"2022_AngewandteChemieInternat_Parvizian.pdf","file_size":1303202,"checksum":"2a3ee0bb59e044b808ebe85cd94ac899","content_type":"application/pdf","access_level":"open_access","date_created":"2022-07-29T09:29:20Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-08-01T00:00:00Z","volume":61,"author":[{"full_name":"Parvizian, Mahsa","last_name":"Parvizian","first_name":"Mahsa"},{"first_name":"Alejandra","full_name":"Duràn Balsa, Alejandra","last_name":"Duràn Balsa"},{"full_name":"Pokratath, Rohan","last_name":"Pokratath","first_name":"Rohan"},{"first_name":"Curran","full_name":"Kalha, Curran","last_name":"Kalha"},{"first_name":"Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho"},{"full_name":"Van Den Eynden, Dietger","last_name":"Van Den Eynden","first_name":"Dietger"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"},{"first_name":"Anna","full_name":"Regoutz, Anna","last_name":"Regoutz"},{"last_name":"De Roo","full_name":"De Roo, Jonathan","first_name":"Jonathan"}],"external_id":{"isi":["000811084000001"],"pmid":["35612297"]},"acknowledgement":"J.D.R. and M.P. acknowledge the SNF Eccellenza funding scheme (project number: 194172). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz Association HGF, for the provision of experimental facilities. Parts of this research were carried out at beamline P21.1, PETRA III. We thank Dr. Soham Banerjee for acquiring the PDF data and helpful advice. A.R. acknowledges the support from the Analytical Chemistry Trust Fund for her CAMS-UK Fellowship. C.K. acknowledges the support from the Department of Chemistry, UCL. The authors acknowledge Dr Stephan Lany from NREL for providing the Cu3N DFT calculations. The authors thank Prof. Raymond Schaak and Dr. Robert William Lord for helpful advice and suggestions regarding the purification procedure. Open access funding provided by Universitat Basel.","status":"public","article_number":"e202207013","article_processing_charge":"No","has_accepted_license":"1","ddc":["540"],"abstract":[{"lang":"eng","text":"The precursor conversion chemistry and surface chemistry of Cu3N and Cu3PdN nanocrystals are unknown or contested. Here, we first obtain phase-pure, colloidally stable nanocubes. Second, we elucidate the pathway by which copper(II) nitrate and oleylamine form Cu3N. We find that oleylamine is both a reductant and a nitrogen source. Oleylamine is oxidized by nitrate to a primary aldimine, which reacts further with excess oleylamine to a secondary aldimine, eliminating ammonia. Ammonia reacts with CuI to form Cu3N. Third, we investigated the surface chemistry and find a mixed ligand shell of aliphatic amines and carboxylates (formed in situ). While the carboxylates appear tightly bound, the amines are easily desorbed from the surface. Finally, we show that doping with palladium decreases the band gap and the material becomes semi-metallic. These results bring insight into the chemistry of metal nitrides and might help the development of other metal nitride nanocrystals."}],"oa":1,"file_date_updated":"2022-07-29T09:29:20Z","related_material":{"record":[{"id":"11695","status":"public","relation":"research_data"}]},"intvolume":"        61","doi":"10.1002/anie.202207013","date_created":"2022-06-19T22:01:58Z","citation":{"ama":"Parvizian M, Duràn Balsa A, Pokratath R, et al. The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. 2022;61(31). doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>","ieee":"M. Parvizian <i>et al.</i>, “The chemistry of Cu₃N and Cu₃PdN nanocrystals,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31. Wiley, 2022.","short":"M. Parvizian, A. Duràn Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van Den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, Angewandte Chemie - International Edition 61 (2022).","ista":"Parvizian M, Duràn Balsa A, Pokratath R, Kalha C, Lee S, Van Den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. The chemistry of Cu₃N and Cu₃PdN nanocrystals. Angewandte Chemie - International Edition. 61(31), e202207013.","apa":"Parvizian, M., Duràn Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van Den Eynden, D., … De Roo, J. (2022). The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>","mla":"Parvizian, Mahsa, et al. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31, e202207013, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>.","chicago":"Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>."},"quality_controlled":"1","scopus_import":"1","day":"01","publication_status":"published","type":"journal_article","publisher":"Wiley","oa_version":"Published Version","month":"08","article_type":"original","date_updated":"2023-08-03T07:19:12Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"MaIb"}],"title":"The chemistry of Cu₃N and Cu₃PdN nanocrystals","_id":"11451","pmid":1,"isi":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]}},{"type":"book_chapter","publication_status":"published","publisher":"Springer Nature","oa_version":"None","series_title":"NM","place":"New York","month":"06","project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","department":[{"_id":"MaDe"}],"date_updated":"2025-04-14T07:43:58Z","publication_identifier":{"isbn":["9781071623206"],"eissn":["1940-6045"],"issn":["0893-2336"],"eisbn":["9781071623213"]},"_id":"11456","ec_funded":1,"page":"277-294","language":[{"iso":"eng"}],"publication":"Behavioral Neurogenetics","year":"2022","acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","status":"public","date_published":"2022-06-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":181,"author":[{"first_name":"Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","full_name":"Artan, Murat"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","first_name":"Mario"}],"abstract":[{"lang":"eng","text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal."}],"editor":[{"last_name":"Yamamoto","full_name":"Yamamoto, Daisuke","first_name":"Daisuke"}],"article_processing_charge":"No","date_created":"2022-06-20T08:10:34Z","citation":{"apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294."},"quality_controlled":"1","scopus_import":"1","day":"04","corr_author":"1","alternative_title":["Neuromethods"],"intvolume":"       181","doi":"10.1007/978-1-0716-2321-3_15"},{"publisher":"Association for Computing Machinery","type":"conference","publication_status":"published","oa_version":"Published Version","arxiv":1,"month":"06","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818"}],"date_updated":"2025-04-14T07:52:47Z","title":"Differential cost analysis with simultaneous potentials and anti-potentials","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)"},"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"ec_funded":1,"_id":"11459","isi":1,"publication_identifier":{"isbn":["9781450392655"]},"year":"2022","page":"442-457","language":[{"iso":"eng"}],"publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","date_published":"2022-06-09T00:00:00Z","file":[{"success":1,"file_name":"2022_PLDI_Zikelic.pdf","file_size":318697,"checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","access_level":"open_access","content_type":"application/pdf","date_created":"2022-06-27T07:38:21Z","date_updated":"2022-06-27T07:38:21Z","creator":"dernst","file_id":"11466","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"author":[{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"},{"first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan","last_name":"Chang"},{"first_name":"Pauline","full_name":"Bolignano, Pauline","last_name":"Bolignano"},{"last_name":"Raimondi","full_name":"Raimondi, Franco","first_name":"Franco"}],"status":"public","acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","article_processing_charge":"No","conference":{"start_date":"2022-06-13","end_date":"2022-06-17","name":"PLDI: Programming Language Design and Implementation","location":"San Diego, CA, United States"},"has_accepted_license":"1","abstract":[{"text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples.","lang":"eng"}],"ddc":["000"],"file_date_updated":"2022-06-27T07:38:21Z","oa":1,"doi":"10.1145/3519939.3523435","scopus_import":"1","quality_controlled":"1","citation":{"apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457."},"date_created":"2022-06-21T09:26:15Z","day":"09","corr_author":"1"},{"title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"SiHi"}],"date_updated":"2025-06-11T13:34:57Z","isi":1,"publication_identifier":{"issn":["2040-2392"]},"_id":"11460","pmid":1,"publication_status":"published","publisher":"Springer Nature","type":"journal_article","oa_version":"Published Version","keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"month":"06","article_type":"original","abstract":[{"lang":"eng","text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life."}],"ddc":["570"],"file_date_updated":"2022-06-24T08:22:59Z","oa":1,"article_processing_charge":"No","article_number":"27","has_accepted_license":"1","scopus_import":"1","date_created":"2022-06-23T14:28:55Z","quality_controlled":"1","citation":{"ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>."},"day":"22","intvolume":"        13","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"doi":"10.1186/s13229-022-00508-3","language":[{"iso":"eng"}],"publication":"Molecular Autism","year":"2022","status":"public","acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-22T00:00:00Z","file":[{"date_updated":"2022-06-24T08:22:59Z","file_id":"11461","creator":"dernst","relation":"main_file","file_name":"2022_MolecularAutism_Schaaf.pdf","success":1,"file_size":7552298,"checksum":"525d2618e855139089bbfc3e3d49d1b2","date_created":"2022-06-24T08:22:59Z","content_type":"application/pdf","access_level":"open_access"}],"author":[{"first_name":"Zachary A.","last_name":"Schaaf","full_name":"Schaaf, Zachary A."},{"full_name":"Tat, Lyvin","last_name":"Tat","first_name":"Lyvin"},{"first_name":"Noemi","full_name":"Cannizzaro, Noemi","last_name":"Cannizzaro"},{"last_name":"Green","full_name":"Green, Ralph","first_name":"Ralph"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"first_name":"Konstantinos S.","last_name":"Zarbalis","full_name":"Zarbalis, Konstantinos S."}],"external_id":{"isi":["000814641400001"],"pmid":["35733184"]},"volume":13},{"date_updated":"2023-10-10T07:15:02Z","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","pmid":1,"_id":"11462","publication_identifier":{"issn":["0175-7598"],"eissn":["1432-0614"]},"isi":1,"oa_version":"None","publication_status":"published","publisher":"Springer Nature","type":"journal_article","article_type":"original","month":"08","article_processing_charge":"No","abstract":[{"text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens.","lang":"eng"}],"doi":"10.1007/s00253-022-12022-w","intvolume":"       106","day":"01","quality_controlled":"1","citation":{"ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>."},"date_created":"2022-06-26T22:01:34Z","scopus_import":"1","year":"2022","publication":"Applied Microbiology and Biotechnology","language":[{"iso":"eng"}],"page":"5093-5103","volume":106,"author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"full_name":"Karputs, Alena","last_name":"Karputs","first_name":"Alena"},{"first_name":"Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976","last_name":"Kavaleuski","full_name":"Kavaleuski, Anton","orcid":"0000-0003-2091-526X"},{"first_name":"Ivan","last_name":"Kuzminski","full_name":"Kuzminski, Ivan"},{"last_name":"Stepanova","full_name":"Stepanova, Elena","first_name":"Elena"},{"first_name":"Andrei","full_name":"Gilep, Andrei","last_name":"Gilep"}],"external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"date_published":"2022-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","status":"public"},{"article_type":"original","project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"}],"month":"06","oa_version":"Published Version","publication_status":"published","publisher":"MDPI","type":"journal_article","pmid":1,"_id":"11489","publication_identifier":{"issn":["1422-0067"]},"isi":1,"date_updated":"2025-04-15T08:12:07Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JiFr"}],"title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"author":[{"first_name":"V","full_name":"Bilanovičová, V","last_name":"Bilanovičová"},{"last_name":"Rýdza","full_name":"Rýdza, N","first_name":"N"},{"full_name":"Koczka, L","last_name":"Koczka","first_name":"L"},{"full_name":"Hess, M","last_name":"Hess","first_name":"M"},{"first_name":"E","last_name":"Feraru","full_name":"Feraru, E"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"T","last_name":"Nodzyński","full_name":"Nodzyński, T"}],"volume":23,"date_published":"2022-06-06T00:00:00Z","file":[{"file_size":2324542,"success":1,"file_name":"2022_IntJMolSci_Bilanovicova.pdf","date_created":"2022-07-06T07:36:59Z","content_type":"application/pdf","access_level":"open_access","checksum":"e997a57a928ec9d51fad8ce824a05935","date_updated":"2022-07-06T07:36:59Z","relation":"main_file","file_id":"11492","creator":"cchlebak"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","year":"2022","issue":"11","language":[{"iso":"eng"}],"publication":"International Journal of Molecular Sciences","page":"6352","doi":"10.3390/ijms23116352","intvolume":"        23","corr_author":"1","day":"06","scopus_import":"1","date_created":"2022-07-05T15:14:34Z","citation":{"mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022."},"quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"Yes","file_date_updated":"2022-07-06T07:36:59Z","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors."}]},{"file_date_updated":"2022-07-08T10:56:52Z","oa":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"GradSch"},{"_id":"SaSi"}],"title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","has_accepted_license":"1","article_processing_charge":"No","date_updated":"2025-04-15T07:27:21Z","corr_author":"1","date_created":"2022-07-08T11:03:02Z","citation":{"apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","short":"R. Schulz, (2022).","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022."},"doi":"10.15479/AT:ISTA:11542","_id":"11542","related_material":{"link":[{"relation":"contains","url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1"}],"record":[{"status":"public","relation":"used_in_publication","id":"11995"}]},"oa_version":"None","year":"2022","contributor":[{"last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","contributor_type":"contact_person","orcid":"0000-0001-8635-0877","first_name":"Sandra"}],"publisher":"Institute of Science and Technology Austria","type":"research_data","status":"public","author":[{"first_name":"Rouven","last_name":"Schulz","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X"}],"date_published":"2022-01-01T00:00:00Z","file":[{"file_size":135784571,"file_name":"Source Data.xlsx","success":1,"access_level":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","date_created":"2022-07-08T10:56:52Z","checksum":"71e8186583f3adbb6c69a88ac9e6e49b","date_updated":"2022-07-08T10:56:52Z","relation":"main_file","creator":"rschulz","file_id":"11543"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"HeEd"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Contravariant pairings between standard Whittaker modules and Verma modules","date_updated":"2025-04-14T07:43:58Z","publication_identifier":{"issn":["0021-8693"]},"isi":1,"ec_funded":1,"_id":"11545","oa_version":"Published Version","publisher":"Elsevier","publication_status":"published","type":"journal_article","keyword":["Algebra and Number Theory"],"article_type":"original","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"month":"11","file_date_updated":"2023-02-02T07:32:48Z","oa":1,"ddc":["510"],"abstract":[{"lang":"eng","text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N ."}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","corr_author":"1","day":"01","scopus_import":"1","date_created":"2022-07-08T11:40:07Z","quality_controlled":"1","citation":{"mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>.","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179.","ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022.","short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>"},"doi":"10.1016/j.jalgebra.2022.06.017","intvolume":"       609","issue":"11","language":[{"iso":"eng"}],"publication":"Journal of Algebra","page":"145-179","year":"2022","acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","status":"public","external_id":{"isi":["000861841100004"]},"author":[{"full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","last_name":"Brown","first_name":"Adam"},{"first_name":"Anna","last_name":"Romanov","full_name":"Romanov, Anna"}],"volume":609,"file":[{"checksum":"82abaee3d7837f703e499a9ecbb25b7c","access_level":"open_access","content_type":"application/pdf","date_created":"2023-02-02T07:32:48Z","file_name":"2022_JournalAlgebra_Brown.pdf","success":1,"file_size":582962,"creator":"dernst","file_id":"12473","relation":"main_file","date_updated":"2023-02-02T07:32:48Z"}],"date_published":"2022-11-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"doi":"10.1098/rstb.2021.0203","intvolume":"       377","corr_author":"1","day":"01","citation":{"ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>"},"quality_controlled":"1","date_created":"2022-07-08T11:41:56Z","scopus_import":"1","has_accepted_license":"1","article_number":"20210203","article_processing_charge":"Yes (via OA deal)","oa":1,"file_date_updated":"2023-02-02T08:20:29Z","ddc":["570"],"abstract":[{"text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.","lang":"eng"}],"volume":377,"external_id":{"pmid":["35694747"],"isi":["000812317300005"]},"author":[{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"file":[{"success":1,"file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","file_size":920304,"checksum":"49f69428f3dcf5ce3ff281f7d199e9df","date_created":"2023-02-02T08:20:29Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-02-02T08:20:29Z","file_id":"12479","creator":"dernst","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-01T00:00:00Z","status":"public","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","year":"2022","issue":"1856","language":[{"iso":"eng"}],"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","pmid":1,"_id":"11546","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"isi":1,"date_updated":"2025-06-12T06:10:18Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Inversions and parallel evolution","article_type":"original","month":"08","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"Snapdragon Speciation"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"oa_version":"Published Version","publisher":"Royal Society of London","type":"journal_article","publication_status":"published"},{"project":[{"call_identifier":"H2020","grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"month":"06","article_type":"original","OA_type":"hybrid","type":"journal_article","publication_status":"published","publisher":"Springer Nature","oa_version":"Published Version","ec_funded":1,"_id":"11553","OA_place":"publisher","publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]},"date_updated":"2025-07-10T11:50:12Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"VaKa"}],"title":"The dynamics of complex box mappings","date_published":"2022-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2022-07-12T10:04:55Z","file_id":"11559","creator":"kschuh","relation":"main_file","success":1,"file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","file_size":2509915,"checksum":"16e7c659dee9073c6c8aeb87316ef201","date_created":"2022-07-12T10:04:55Z","access_level":"open_access","content_type":"application/pdf"}],"author":[{"last_name":"Clark","full_name":"Clark, Trevor","first_name":"Trevor"},{"first_name":"Kostiantyn","full_name":"Drach, Kostiantyn","orcid":"0000-0002-9156-8616","last_name":"Drach","id":"fe8209e2-906f-11eb-847d-950f8fc09115"},{"first_name":"Oleg","last_name":"Kozlovski","full_name":"Kozlovski, Oleg"},{"first_name":"Sebastian Van","full_name":"Strien, Sebastian Van","last_name":"Strien"}],"volume":8,"status":"public","acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions.","year":"2022","publication":"Arnold Mathematical Journal","language":[{"iso":"eng"}],"page":"319-410","issue":"2","intvolume":"         8","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00209-y"},{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00218-x"}]},"doi":"10.1007/s40598-022-00200-7","scopus_import":"1","citation":{"ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022.","short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410.","ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410.","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>.","chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>"},"date_created":"2022-07-10T22:01:53Z","quality_controlled":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","ddc":["500"],"abstract":[{"text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.","lang":"eng"}],"file_date_updated":"2022-07-12T10:04:55Z","oa":1},{"intvolume":"       467","doi":"10.1016/j.jcp.2022.111439","quality_controlled":"1","date_created":"2022-07-11T12:19:59Z","citation":{"ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>."},"scopus_import":"1","day":"15","article_number":"111439","article_processing_charge":"No","abstract":[{"text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise.","lang":"eng"}],"ddc":["518"],"oa":1,"date_published":"2022-10-15T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":467,"external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"author":[{"orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","first_name":"Aleksei"},{"last_name":"Osinskiy","full_name":"Osinskiy, A.I.","first_name":"A.I."},{"last_name":"Matveev","full_name":"Matveev, S.A.","first_name":"S.A."},{"first_name":"W.","full_name":"Otieno, W.","last_name":"Otieno"},{"first_name":"N.V.","full_name":"Brilliantov, N.V.","last_name":"Brilliantov"}],"acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","status":"public","year":"2022","publication":"Journal of Computational Physics","language":[{"iso":"eng"}],"_id":"11556","isi":1,"publication_identifier":{"issn":["0021-9991"]},"date_updated":"2024-10-21T06:01:47Z","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"month":"10","article_type":"original","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.09481","open_access":"1"}],"type":"journal_article","publication_status":"published","publisher":"Elsevier","oa_version":"Preprint","arxiv":1}]