[{"acknowledged_ssus":[{"_id":"NanoFab"}],"article_number":"044054","quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"id":"14520","status":"public","relation":"research_data"}]},"date_updated":"2024-08-07T07:11:55Z","doi":"10.1103/PhysRevApplied.20.044054","article_processing_charge":"No","date_published":"2023-10-20T00:00:00Z","author":[{"first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628"},{"first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea","last_name":"Trioni"},{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","intvolume":"        20","main_file_link":[{"url":"https://arxiv.org/abs/2206.14104","open_access":"1"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"F07105","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"},{"_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738","name":"Open Superconducting Quantum Computers (OpenSuperQPlus)","grant_number":"101080139"}],"month":"10","day":"20","oa_version":"Preprint","ec_funded":1,"date_created":"2023-11-12T23:00:55Z","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"title":"Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses","publication":"Physical Review Applied","abstract":[{"lang":"eng","text":"State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with  100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. "}],"arxiv":1,"year":"2023","_id":"14517","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":20,"publication_identifier":{"eissn":["2331-7019"]},"citation":{"ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. <i>Physical Review Applied</i>. 2023;20(4). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">10.1103/PhysRevApplied.20.044054</a>","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023).","mla":"Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” <i>Physical Review Applied</i>, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">10.1103/PhysRevApplied.20.044054</a>.","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">https://doi.org/10.1103/PhysRevApplied.20.044054</a>.","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” <i>Physical Review Applied</i>, vol. 20, no. 4. American Physical Society, 2023.","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">https://doi.org/10.1103/PhysRevApplied.20.044054</a>"},"external_id":{"arxiv":["2206.14104"]},"article_type":"original","issue":"4","status":"public","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility.","oa":1},{"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"month":"09","day":"28","ddc":["000"],"publication_status":"published","file":[{"checksum":"1390ca38480fa4cf286b0f1a42e8c12f","file_name":"2023_FAIA_Avni.pdf","file_size":501011,"date_updated":"2023-11-13T10:16:10Z","file_id":"14529","date_created":"2023-11-13T10:16:10Z","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file"}],"intvolume":"       372","license":"https://creativecommons.org/licenses/by-nc/4.0/","quality_controlled":"1","scopus_import":"1","date_updated":"2025-07-14T09:09:57Z","doi":"10.3233/FAIA230264","article_processing_charge":"No","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","last_name":"Avni","orcid":"0000-0001-5588-8287","first_name":"Guy"},{"last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"full_name":"Sadhukhan, Suman","last_name":"Sadhukhan","first_name":"Suman"},{"full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684"},{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"date_published":"2023-09-28T00:00:00Z","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"conference":{"start_date":"2023-09-30","location":"Krakow, Poland","end_date":"2023-10-04","name":"ECAI: European Conference on Artificial Intelligence"},"file_date_updated":"2023-11-13T10:16:10Z","publication_identifier":{"issn":["0922-6389"],"isbn":["9781643684369"]},"citation":{"ama":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman discrete-bidding games. In: <i>Frontiers in Artificial Intelligence and Applications</i>. Vol 372. IOS Press; 2023:141-148. doi:<a href=\"https://doi.org/10.3233/FAIA230264\">10.3233/FAIA230264</a>","ista":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications. ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.","mla":"Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” <i>Frontiers in Artificial Intelligence and Applications</i>, vol. 372, IOS Press, 2023, pp. 141–48, doi:<a href=\"https://doi.org/10.3233/FAIA230264\">10.3233/FAIA230264</a>.","short":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.","chicago":"Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde Zikelic. “Reachability Poorman Discrete-Bidding Games.” In <i>Frontiers in Artificial Intelligence and Applications</i>, 372:141–48. IOS Press, 2023. <a href=\"https://doi.org/10.3233/FAIA230264\">https://doi.org/10.3233/FAIA230264</a>.","ieee":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability poorman discrete-bidding games,” in <i>Frontiers in Artificial Intelligence and Applications</i>, Krakow, Poland, 2023, vol. 372, pp. 141–148.","apa":"Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., &#38; Zikelic, D. (2023). Reachability poorman discrete-bidding games. In <i>Frontiers in Artificial Intelligence and Applications</i> (Vol. 372, pp. 141–148). Krakow, Poland: IOS Press. <a href=\"https://doi.org/10.3233/FAIA230264\">https://doi.org/10.3233/FAIA230264</a>"},"external_id":{"arxiv":["2307.15218"]},"oa":1,"acknowledgement":"This research was supported in part by ISF grant no. 1679/21, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.","status":"public","year":"2023","has_accepted_license":"1","_id":"14518","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"141-148","volume":372,"abstract":[{"lang":"eng","text":"We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets."}],"arxiv":1,"oa_version":"Published Version","date_created":"2023-11-12T23:00:56Z","ec_funded":1,"publisher":"IOS Press","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Reachability poorman discrete-bidding games","publication":"Frontiers in Artificial Intelligence and Applications"},{"year":"2023","_id":"14523","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8329143"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","month":"09","citation":{"short":"J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023).","ista":"Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>.","mla":"Binysh, Jack, et al. <i>SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>.","ama":"Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8329143\">10.5281/ZENODO.8329143</a>","apa":"Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., &#38; Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8329143\">https://doi.org/10.5281/ZENODO.8329143</a>","chicago":"Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8329143\">https://doi.org/10.5281/ZENODO.8329143</a>.","ieee":"J. Binysh <i>et al.</i>, “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023."},"ddc":["530"],"day":"08","oa":1,"status":"public","date_created":"2023-11-13T09:12:11Z","oa_version":"Published Version","publisher":"Zenodo","department":[{"_id":"ScWa"}],"title":"SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1","abstract":[{"lang":"eng","text":"see Readme file"}],"article_processing_charge":"No","date_updated":"2023-11-13T09:21:31Z","related_material":{"record":[{"id":"14514","status":"public","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.8329143","author":[{"full_name":"Binysh, Jack","last_name":"Binysh","first_name":"Jack"},{"first_name":"Indrajit","last_name":"Chakraborty","full_name":"Chakraborty, Indrajit"},{"first_name":"Mykyta","last_name":"Chubynsky","full_name":"Chubynsky, Mykyta"},{"first_name":"Vicente L","last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","first_name":"Scott R"},{"last_name":"Sprittles","first_name":"James","full_name":"Sprittles, James"},{"full_name":"Souslov, Anton","last_name":"Souslov","first_name":"Anton"}],"date_published":"2023-09-08T00:00:00Z"},{"page":"260","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"_id":"14530","has_accepted_license":"1","year":"2023","oa":1,"status":"public","citation":{"apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14530\">https://doi.org/10.15479/14530</a>.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/14530\">10.15479/14530</a>"},"publication_identifier":{"issn":["2663 - 337X"]},"department":[{"_id":"GradSch"},{"_id":"MiSi"}],"title":"Synchronization in collectively moving active matter","publisher":"Institute of Science and Technology Austria","oa_version":"Updated Version","date_created":"2023-11-15T09:59:03Z","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order.  In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.  "}],"publication_status":"published","file":[{"file_id":"14536","date_updated":"2023-11-15T09:52:54Z","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","file_name":"Thesis_Riedl_2023_corr.pdf","file_size":36743942,"creator":"mriedl","access_level":"open_access","relation":"main_file","date_created":"2023-11-15T09:52:54Z","success":1,"content_type":"application/pdf"}],"day":"16","ddc":["530","570"],"language":[{"iso":"eng"}],"month":"11","file_date_updated":"2023-11-15T09:52:54Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","first_name":"Michael"}],"date_published":"2023-11-16T00:00:00Z","alternative_title":["ISTA Thesis"],"doi":"10.15479/14530","date_updated":"2023-11-30T10:55:13Z","related_material":{"record":[{"id":"10703","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"id":"7932","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"461"},{"status":"public","relation":"old_edition","id":"12726"}]},"article_processing_charge":"No","degree_awarded":"PhD","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"file_date_updated":"2023-11-15T13:44:24Z","degree_awarded":"PhD","date_published":"2023-11-15T00:00:00Z","author":[{"last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"related_material":{"record":[{"id":"1194","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"12000"},{"id":"12511","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14600"},{"status":"public","relation":"part_of_dissertation","id":"14601"},{"id":"9644","relation":"part_of_dissertation","status":"public"},{"id":"10414","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2025-07-14T09:10:10Z","doi":"10.15479/14539","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","publication_status":"published","file":[{"file_size":2116426,"checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_name":"main.pdf","file_id":"14540","date_updated":"2023-11-15T13:43:28Z","content_type":"application/pdf","date_created":"2023-11-15T13:43:28Z","success":1,"relation":"main_file","creator":"cchlebak","access_level":"open_access"},{"date_created":"2023-11-15T13:44:24Z","content_type":"application/x-zip-compressed","creator":"cchlebak","access_level":"closed","relation":"source_file","checksum":"80ca37618a3c7b59866875f8be9b15ed","file_name":"thesis_source.zip","file_size":35884057,"date_updated":"2023-11-15T13:44:24Z","file_id":"14541"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"11","day":"15","ddc":["000"],"oa_version":"Published Version","date_created":"2023-11-15T13:39:10Z","ec_funded":1,"title":"Automated verification and control of infinite state stochastic systems","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"_id":"14539","supervisor":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"year":"2023","page":"256","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>","mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>"},"publication_identifier":{"isbn":["978-3-99078-036-7"],"issn":["2663 - 337X"]},"oa":1,"status":"public"},{"main_file_link":[{"url":"https://doi.org/10.1142/S0129055X2360005X","open_access":"1"}],"publication_status":"epub_ahead","month":"10","language":[{"iso":"eng"}],"project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"day":"31","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"2360005 ","scopus_import":"1","quality_controlled":"1","date_published":"2023-10-31T00:00:00Z","author":[{"id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha","last_name":"Henheik","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard"},{"orcid":"0000-0002-9071-5880","last_name":"Roos","first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","full_name":"Roos, Barbara"}],"article_processing_charge":"Yes (in subscription journal)","doi":"10.1142/s0129055x2360005x","date_updated":"2023-11-20T10:04:38Z","_id":"14542","year":"2023","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>, 2360005, World Scientific Publishing, 2023, doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>.","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. 2023. doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>","apa":"Henheik, S. J., Lauritsen, A. B., &#38; Roos, B. (2023). Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023.","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2023. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>."},"publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"oa":1,"status":"public","acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges  partial  financial  support  by  the  ERC  Advanced  Grant  “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","external_id":{"arxiv":["2301.05621"]},"article_type":"original","date_created":"2023-11-15T23:48:14Z","ec_funded":1,"oa_version":"Published Version","publication":"Reviews in Mathematical Physics","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"title":"Universality in low-dimensional BCS theory","publisher":"World Scientific Publishing","abstract":[{"lang":"eng","text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."}],"arxiv":1},{"title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","department":[{"_id":"GradSch"}],"publication":"Brain","publisher":"Oxford University Press","oa_version":"Submitted Version","date_created":"2023-11-16T12:36:51Z","abstract":[{"lang":"eng","text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders."}],"extern":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14543","year":"2023","oa":1,"status":"public","article_type":"original","citation":{"apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. <i>Brain</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awad380\">https://doi.org/10.1093/brain/awad380</a>","ieee":"R. Kaiyrzhanov <i>et al.</i>, “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” <i>Brain</i>. Oxford University Press, 2023.","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/brain/awad380\">https://doi.org/10.1093/brain/awad380</a>.","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).","ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain., awad380.","mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” <i>Brain</i>, awad380, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/brain/awad380\">10.1093/brain/awad380</a>.","ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. <i>Brain</i>. 2023. doi:<a href=\"https://doi.org/10.1093/brain/awad380\">10.1093/brain/awad380</a>"},"publication_identifier":{"eissn":["1460-2156"],"issn":["0006-8950"]},"article_number":"awad380","date_published":"2023-11-10T00:00:00Z","author":[{"full_name":"Kaiyrzhanov, Rauan","first_name":"Rauan","last_name":"Kaiyrzhanov"},{"full_name":"Rad, Aboulfazl","first_name":"Aboulfazl","last_name":"Rad"},{"first_name":"Sheng-Jia","last_name":"Lin","full_name":"Lin, Sheng-Jia"},{"last_name":"Bertoli-Avella","first_name":"Aida","full_name":"Bertoli-Avella, Aida"},{"last_name":"Kallemeijn","first_name":"Wouter W","full_name":"Kallemeijn, Wouter W"},{"first_name":"Annie","last_name":"Godwin","full_name":"Godwin, Annie"},{"full_name":"Zaki, Maha S","first_name":"Maha S","last_name":"Zaki"},{"first_name":"Kevin","last_name":"Huang","orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3"},{"full_name":"Lau, Tracy","first_name":"Tracy","last_name":"Lau"},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"full_name":"Efthymiou, Stephanie","last_name":"Efthymiou","first_name":"Stephanie"},{"full_name":"Ghayoor Karimiani, Ehsan","first_name":"Ehsan","last_name":"Ghayoor Karimiani"},{"first_name":"Maja","last_name":"Hempel","full_name":"Hempel, Maja"},{"full_name":"Normand, Elizabeth A","first_name":"Elizabeth A","last_name":"Normand"},{"last_name":"Rudnik-Schöneborn","first_name":"Sabine","full_name":"Rudnik-Schöneborn, Sabine"},{"last_name":"Schatz","first_name":"Ulrich A","full_name":"Schatz, Ulrich A"},{"first_name":"Marc P","last_name":"Baggelaar","full_name":"Baggelaar, Marc P"},{"full_name":"Ilyas, Muhammad","first_name":"Muhammad","last_name":"Ilyas"},{"first_name":"Tipu","last_name":"Sultan","full_name":"Sultan, Tipu"},{"full_name":"Alvi, Javeria Raza","first_name":"Javeria Raza","last_name":"Alvi"},{"full_name":"Ganieva, Manizha","last_name":"Ganieva","first_name":"Manizha"},{"full_name":"Fowler, Ben","first_name":"Ben","last_name":"Fowler"},{"full_name":"Aanicai, Ruxandra","last_name":"Aanicai","first_name":"Ruxandra"},{"first_name":"Gulsen","last_name":"Akay Tayfun","full_name":"Akay Tayfun, Gulsen"},{"full_name":"Al Saman, Abdulaziz","last_name":"Al Saman","first_name":"Abdulaziz"},{"full_name":"Alswaid, Abdulrahman","first_name":"Abdulrahman","last_name":"Alswaid"},{"full_name":"Amiri, Nafise","first_name":"Nafise","last_name":"Amiri"},{"full_name":"Asilova, Nilufar","last_name":"Asilova","first_name":"Nilufar"},{"first_name":"Vorasuk","last_name":"Shotelersuk","full_name":"Shotelersuk, Vorasuk"},{"full_name":"Yeetong, Patra","first_name":"Patra","last_name":"Yeetong"},{"full_name":"Azam, Matloob","last_name":"Azam","first_name":"Matloob"},{"full_name":"Babaei, Meisam","last_name":"Babaei","first_name":"Meisam"},{"last_name":"Bahrami Monajemi","first_name":"Gholamreza","full_name":"Bahrami Monajemi, Gholamreza"},{"full_name":"Mohammadi, Pouria","first_name":"Pouria","last_name":"Mohammadi"},{"full_name":"Samie, Saeed","last_name":"Samie","first_name":"Saeed"},{"full_name":"Banu, Selina Husna","first_name":"Selina Husna","last_name":"Banu"},{"full_name":"Basto, Jorge Pinto","last_name":"Basto","first_name":"Jorge Pinto"},{"last_name":"Kortüm","first_name":"Fanny","full_name":"Kortüm, Fanny"},{"first_name":"Mislen","last_name":"Bauer","full_name":"Bauer, Mislen"},{"full_name":"Bauer, Peter","last_name":"Bauer","first_name":"Peter"},{"full_name":"Beetz, Christian","last_name":"Beetz","first_name":"Christian"},{"first_name":"Masoud","last_name":"Garshasbi","full_name":"Garshasbi, Masoud"},{"full_name":"Hameed Issa, Awatif","last_name":"Hameed Issa","first_name":"Awatif"},{"full_name":"Eyaid, Wafaa","last_name":"Eyaid","first_name":"Wafaa"},{"full_name":"Ahmed, Hind","first_name":"Hind","last_name":"Ahmed"},{"first_name":"Narges","last_name":"Hashemi","full_name":"Hashemi, Narges"},{"first_name":"Kazem","last_name":"Hassanpour","full_name":"Hassanpour, Kazem"},{"full_name":"Herman, Isabella","first_name":"Isabella","last_name":"Herman"},{"full_name":"Ibrohimov, Sherozjon","first_name":"Sherozjon","last_name":"Ibrohimov"},{"last_name":"Abdul-Majeed","first_name":"Ban A","full_name":"Abdul-Majeed, Ban A"},{"first_name":"Maria","last_name":"Imdad","full_name":"Imdad, Maria"},{"full_name":"Isrofilov, Maksudjon","first_name":"Maksudjon","last_name":"Isrofilov"},{"first_name":"Qassem","last_name":"Kaiyal","full_name":"Kaiyal, Qassem"},{"full_name":"Khan, Suliman","last_name":"Khan","first_name":"Suliman"},{"first_name":"Brian","last_name":"Kirmse","full_name":"Kirmse, Brian"},{"full_name":"Koster, Janet","first_name":"Janet","last_name":"Koster"},{"full_name":"Lourenço, Charles Marques","last_name":"Lourenço","first_name":"Charles Marques"},{"full_name":"Mitani, Tadahiro","first_name":"Tadahiro","last_name":"Mitani"},{"first_name":"Oana","last_name":"Moldovan","full_name":"Moldovan, Oana"},{"first_name":"David","last_name":"Murphy","full_name":"Murphy, David"},{"last_name":"Najafi","first_name":"Maryam","full_name":"Najafi, Maryam"},{"full_name":"Pehlivan, Davut","first_name":"Davut","last_name":"Pehlivan"},{"last_name":"Rocha","first_name":"Maria Eugenia","full_name":"Rocha, Maria Eugenia"},{"full_name":"Salpietro, Vincenzo","first_name":"Vincenzo","last_name":"Salpietro"},{"first_name":"Miriam","last_name":"Schmidts","full_name":"Schmidts, Miriam"},{"full_name":"Shalata, Adel","last_name":"Shalata","first_name":"Adel"},{"full_name":"Mahroum, Mohammad","first_name":"Mohammad","last_name":"Mahroum"},{"first_name":"Jawabreh Kassem","last_name":"Talbeya","full_name":"Talbeya, Jawabreh Kassem"},{"full_name":"Taylor, Robert W","last_name":"Taylor","first_name":"Robert W"},{"last_name":"Vazquez","first_name":"Dayana","full_name":"Vazquez, Dayana"},{"full_name":"Vetro, Annalisa","first_name":"Annalisa","last_name":"Vetro"},{"full_name":"Waterham, Hans R","last_name":"Waterham","first_name":"Hans R"},{"full_name":"Zaman, Mashaya","first_name":"Mashaya","last_name":"Zaman"},{"last_name":"Schrader","first_name":"Tina A","full_name":"Schrader, Tina A"},{"last_name":"Chung","first_name":"Wendy K","full_name":"Chung, Wendy K"},{"full_name":"Guerrini, Renzo","last_name":"Guerrini","first_name":"Renzo"},{"first_name":"James R","last_name":"Lupski","full_name":"Lupski, James R"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"},{"first_name":"Mohnish","last_name":"Suri","full_name":"Suri, Mohnish"},{"full_name":"Jamshidi, Yalda","first_name":"Yalda","last_name":"Jamshidi"},{"full_name":"Bhatia, Kailash P","last_name":"Bhatia","first_name":"Kailash P"},{"last_name":"Vona","first_name":"Barbara","full_name":"Vona, Barbara"},{"full_name":"Schrader, Michael","first_name":"Michael","last_name":"Schrader"},{"first_name":"Mariasavina","last_name":"Severino","full_name":"Severino, Mariasavina"},{"full_name":"Guille, Matthew","last_name":"Guille","first_name":"Matthew"},{"full_name":"Tate, Edward W","first_name":"Edward W","last_name":"Tate"},{"full_name":"Varshney, Gaurav K","first_name":"Gaurav K","last_name":"Varshney"},{"full_name":"Houlden, Henry","last_name":"Houlden","first_name":"Henry"},{"last_name":"Maroofian","first_name":"Reza","full_name":"Maroofian, Reza"}],"date_updated":"2023-11-20T10:17:32Z","doi":"10.1093/brain/awad380","article_processing_charge":"No","scopus_import":"1","keyword":["Neurology (clinical)"],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awad380"}],"publication_status":"epub_ahead","day":"10","language":[{"iso":"eng"}],"month":"11"},{"oa_version":"Published Version","date_created":"2023-11-17T13:45:26Z","title":"Resonant microwave spectroscopy of Al-InAs","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"supervisor":[{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"}],"_id":"14547","has_accepted_license":"1","year":"2023","page":"80","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>","mla":"Phan, Duc T. <i>Resonant Microwave Spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>.","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>.","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","apa":"Phan, D. T. (2023). <i>Resonant microwave spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>"},"publication_identifier":{"issn":["2663 - 337X"]},"oa":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"file_date_updated":"2023-11-22T09:46:06Z","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"degree_awarded":"PhD","author":[{"full_name":"Phan, Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan"}],"date_published":"2023-11-16T00:00:00Z","doi":"10.15479/14547","date_updated":"2023-11-30T10:56:04Z","related_material":{"record":[{"id":"10851","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"13264"}]},"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","publication_status":"published","file":[{"date_created":"2023-11-17T13:36:44Z","content_type":"application/pdf","creator":"pduc","access_level":"open_access","relation":"main_file","file_name":"Phan_Thesis_pdfa.pdf","checksum":"db0c37d213bc002125bd59690e9db246","file_size":34828019,"file_id":"14548","date_updated":"2023-11-22T09:46:06Z"},{"date_updated":"2023-11-17T13:47:54Z","file_id":"14549","file_size":279319709,"checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","file_name":"dissertation_src.zip","relation":"source_file","creator":"pduc","access_level":"closed","content_type":"application/zip","date_created":"2023-11-17T13:44:53Z"}],"language":[{"iso":"eng"}],"month":"11","day":"16","ddc":["530"]},{"publication_status":"published","file":[{"file_size":5587897,"file_name":"2023_CellSystems_Briffa.pdf","checksum":"101fdac59e6f1102d68ef91f2b5bd51a","date_updated":"2023-11-20T11:22:52Z","file_id":"14580","content_type":"application/pdf","success":1,"date_created":"2023-11-20T11:22:52Z","relation":"main_file","creator":"dernst","access_level":"open_access"}],"intvolume":"        14","project":[{"_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","name":"Quantitative analysis of DNA methylation maintenance with chromatin","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"month":"11","day":"15","ddc":["570"],"pmid":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-11-20T11:22:52Z","quality_controlled":"1","scopus_import":"1","date_updated":"2023-11-20T11:24:34Z","doi":"10.1016/j.cels.2023.10.007","article_processing_charge":"Yes (via OA deal)","date_published":"2023-11-15T00:00:00Z","author":[{"full_name":"Briffa, Amy","last_name":"Briffa","first_name":"Amy"},{"id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth","last_name":"Hollwey","first_name":"Elizabeth"},{"last_name":"Shahzad","first_name":"Zaigham","full_name":"Shahzad, Zaigham"},{"last_name":"Moore","first_name":"Jonathan D.","full_name":"Moore, Jonathan D."},{"first_name":"David B.","last_name":"Lyons","full_name":"Lyons, David B."},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"has_accepted_license":"1","year":"2023","_id":"14551","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"953-967","volume":14,"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"citation":{"chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>.","ieee":"A. Briffa <i>et al.</i>, “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” <i>Cell Systems</i>, vol. 14, no. 11. Elsevier, pp. 953–967, 2023.","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., &#38; Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">https://doi.org/10.1016/j.cels.2023.10.007</a>","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. <i>Cell Systems</i>. 2023;14(11):953-967. doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>","short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.","mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” <i>Cell Systems</i>, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:<a href=\"https://doi.org/10.1016/j.cels.2023.10.007\">10.1016/j.cels.2023.10.007</a>."},"article_type":"original","external_id":{"pmid":["37944515"]},"issue":"11","acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","status":"public","oa":1,"oa_version":"Published Version","date_created":"2023-11-19T23:00:54Z","ec_funded":1,"publisher":"Elsevier","department":[{"_id":"DaZi"}],"title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","publication":"Cell Systems","abstract":[{"lang":"eng","text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale."}]},{"citation":{"mla":"Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” <i>Physical Review A</i>, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">10.1103/PhysRevA.108.042430</a>.","ista":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023).","ama":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. <i>Physical Review A</i>. 2023;108(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">10.1103/PhysRevA.108.042430</a>","apa":"Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., &#38; Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">https://doi.org/10.1103/PhysRevA.108.042430</a>","chicago":"Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.108.042430\">https://doi.org/10.1103/PhysRevA.108.042430</a>.","ieee":"E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” <i>Physical Review A</i>, vol. 108, no. 4. American Physical Society, 2023."},"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"oa":1,"status":"public","issue":"4","article_type":"original","external_id":{"arxiv":["2212.07406"]},"_id":"14553","year":"2023","volume":108,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","abstract":[{"text":"Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.","lang":"eng"}],"arxiv":1,"date_created":"2023-11-19T23:00:54Z","oa_version":"Preprint","publication":"Physical Review A","title":"Continuous-variable quantum tomography of high-amplitude states","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","month":"10","language":[{"iso":"eng"}],"day":"30","intvolume":"       108","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.07406"}],"publication_status":"published","scopus_import":"1","quality_controlled":"1","date_published":"2023-10-30T00:00:00Z","author":[{"last_name":"Fedotova","orcid":"0000-0001-7242-015X","first_name":"Ekaterina","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab","full_name":"Fedotova, Ekaterina"},{"first_name":"Nikolai","last_name":"Kuznetsov","full_name":"Kuznetsov, Nikolai"},{"full_name":"Tiunov, Egor","first_name":"Egor","last_name":"Tiunov"},{"first_name":"A. E.","last_name":"Ulanov","full_name":"Ulanov, A. E."},{"last_name":"Lvovsky","first_name":"A. I.","full_name":"Lvovsky, A. I."}],"article_processing_charge":"No","date_updated":"2023-11-20T10:26:51Z","doi":"10.1103/PhysRevA.108.042430","article_number":"042430"},{"intvolume":"        57","file":[{"success":1,"date_created":"2023-11-20T08:34:57Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","file_name":"2023_ESAIM_Cornalba.pdf","checksum":"3aef1475b1882c8dec112df9a5167c39","file_size":1508534,"file_id":"14560","date_updated":"2023-11-20T08:34:57Z"}],"publication_status":"published","ddc":["510"],"day":"01","month":"09","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"file_date_updated":"2023-11-20T08:34:57Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"id":"2CEB641C-A400-11E9-A717-D712E6697425","full_name":"Cornalba, Federico","last_name":"Cornalba","orcid":"0000-0002-6269-5149","first_name":"Federico"},{"full_name":"Shardlow, Tony","first_name":"Tony","last_name":"Shardlow"}],"date_published":"2023-09-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","doi":"10.1051/m2an/2023077","date_updated":"2023-11-20T08:38:47Z","related_material":{"link":[{"relation":"software","url":"https://github.com/tonyshardlow/RIDK-FD"}]},"scopus_import":"1","quality_controlled":"1","volume":57,"page":"3061-3090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"14554","year":"2023","has_accepted_license":"1","oa":1,"acknowledgement":"The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project).","status":"public","issue":"5","article_type":"original","citation":{"apa":"Cornalba, F., &#38; Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/m2an/2023077\">https://doi.org/10.1051/m2an/2023077</a>","ieee":"F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023.","chicago":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/m2an/2023077\">https://doi.org/10.1051/m2an/2023077</a>.","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","mla":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:<a href=\"https://doi.org/10.1051/m2an/2023077\">10.1051/m2an/2023077</a>.","ista":"Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.","ama":"Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. <i>ESAIM: Mathematical Modelling and Numerical Analysis</i>. 2023;57(5):3061-3090. doi:<a href=\"https://doi.org/10.1051/m2an/2023077\">10.1051/m2an/2023077</a>"},"publication_identifier":{"issn":["2822-7840"],"eissn":["2804-7214"]},"publication":"ESAIM: Mathematical Modelling and Numerical Analysis","department":[{"_id":"JuFi"}],"title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","publisher":"EDP Sciences","date_created":"2023-11-19T23:00:55Z","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format."}]},{"abstract":[{"text":"The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-11-19T23:00:55Z","publisher":"Frontiers","department":[{"_id":"MiSi"}],"title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","publication":"Frontiers in Cell and Developmental Biology","publication_identifier":{"eissn":["2296-634X"]},"citation":{"mla":"Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 11, 1287420, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fcell.2023.1287420\">10.3389/fcell.2023.1287420</a>.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","ista":"Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420.","ama":"Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. <i>Frontiers in Cell and Developmental Biology</i>. 2023;11. doi:<a href=\"https://doi.org/10.3389/fcell.2023.1287420\">10.3389/fcell.2023.1287420</a>","apa":"Riedl, M., &#38; Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fcell.2023.1287420\">https://doi.org/10.3389/fcell.2023.1287420</a>","chicago":"Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fcell.2023.1287420\">https://doi.org/10.3389/fcell.2023.1287420</a>.","ieee":"M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 11. Frontiers, 2023."},"article_type":"original","oa":1,"acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","status":"public","has_accepted_license":"1","year":"2023","_id":"14555","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":11,"quality_controlled":"1","scopus_import":"1","doi":"10.3389/fcell.2023.1287420","date_updated":"2023-11-20T08:44:17Z","article_processing_charge":"Yes","date_published":"2023-10-31T00:00:00Z","author":[{"full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"1287420","file_date_updated":"2023-11-20T08:41:15Z","language":[{"iso":"eng"}],"month":"10","day":"31","ddc":["570"],"publication_status":"published","file":[{"date_updated":"2023-11-20T08:41:15Z","file_id":"14561","checksum":"61857fc3ebf019354932e7ee684658ce","file_name":"2023_FrontiersCellDevBio_Riedl.pdf","file_size":2047622,"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2023-11-20T08:41:15Z","success":1,"content_type":"application/pdf"}],"intvolume":"        11"},{"abstract":[{"lang":"eng","text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach."}],"date_created":"2023-11-19T23:00:55Z","oa_version":"Published Version","publisher":"Wiley","publication":"Journal of Evolutionary Biology","title":"How chromosomal inversions reorient the evolutionary process","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"citation":{"chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/jeb.14242\">https://doi.org/10.1111/jeb.14242</a>.","ieee":"E. L. Berdan <i>et al.</i>, “How chromosomal inversions reorient the evolutionary process,” <i>Journal of Evolutionary Biology</i>. Wiley, 2023.","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14242\">https://doi.org/10.1111/jeb.14242</a>","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. <i>Journal of Evolutionary Biology</i>. 2023. doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” <i>Journal of Evolutionary Biology</i>, 14242, Wiley, 2023, doi:<a href=\"https://doi.org/10.1111/jeb.14242\">10.1111/jeb.14242</a>."},"article_type":"review","oa":1,"status":"public","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","year":"2023","has_accepted_license":"1","_id":"14556","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","date_updated":"2023-11-20T08:51:09Z","doi":"10.1111/jeb.14242","date_published":"2023-11-08T00:00:00Z","author":[{"full_name":"Berdan, Emma L.","last_name":"Berdan","first_name":"Emma L."},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Charlesworth, Brian","first_name":"Brian","last_name":"Charlesworth"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Fragata, Inês","first_name":"Inês","last_name":"Fragata"},{"last_name":"Gilbert","first_name":"Kimberly J.","full_name":"Gilbert, Kimberly J."},{"first_name":"Paul","last_name":"Jay","full_name":"Jay, Paul"},{"full_name":"Kapun, Martin","first_name":"Martin","last_name":"Kapun"},{"last_name":"Lotterhos","first_name":"Katie E.","full_name":"Lotterhos, Katie E."},{"first_name":"Claire","last_name":"Mérot","full_name":"Mérot, Claire"},{"full_name":"Durmaz Mitchell, Esra","first_name":"Esra","last_name":"Durmaz Mitchell"},{"last_name":"Pascual","first_name":"Marta","full_name":"Pascual, Marta"},{"first_name":"Catherine L.","last_name":"Peichel","full_name":"Peichel, Catherine L."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"full_name":"Schaeffer, Stephen W.","first_name":"Stephen W.","last_name":"Schaeffer"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Thomas","last_name":"Flatt","full_name":"Flatt, Thomas"}],"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_number":"14242","month":"11","language":[{"iso":"eng"}],"ddc":["570"],"day":"08","publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.1111/jeb.14242","open_access":"1"}]},{"citation":{"short":"F.K. Schur, (2023).","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","mla":"Schur, Florian KM. <i>Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14562\">10.15479/AT:ISTA:14562</a>","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14562\">https://doi.org/10.15479/AT:ISTA:14562</a>."},"status":"public","oa":1,"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","_id":"14562","year":"2023","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"last_name":"Fäßler","orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"first_name":"Manjunath","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","contributor_type":"researcher"},{"contributor_type":"researcher","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler","orcid":"0000-0002-3616-8580","first_name":"Julia"},{"contributor_type":"researcher","first_name":"Hermann","last_name":"Döring"},{"contributor_type":"researcher","id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","first_name":"Florian","last_name":"Hofer"},{"first_name":"Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","contributor_type":"researcher","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","contributor_type":"researcher","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Faix","contributor_type":"researcher"},{"first_name":"Klemens","last_name":"Rottner","contributor_type":"researcher"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","contributor_type":"researcher","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"date_created":"2023-11-20T09:22:33Z","oa_version":"Published Version","department":[{"_id":"FlSc"}],"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","publisher":"Institute of Science and Technology Austria","month":"11","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"ddc":["570"],"day":"21","file":[{"file_id":"14570","date_updated":"2023-11-20T10:27:17Z","file_size":1581687449,"checksum":"e9bab797b44614f144a5b02d9636f8c3","file_name":"Figure2.zip","relation":"main_file","creator":"fschur","access_level":"open_access","content_type":"application/zip","date_created":"2023-11-20T10:27:17Z","success":1},{"date_created":"2023-11-20T10:29:18Z","success":1,"content_type":"application/zip","creator":"fschur","access_level":"open_access","relation":"main_file","checksum":"4efd388cccd03c549fc90f6e46d37006","file_name":"SupplementaryFigure3.zip","file_size":116088565,"date_updated":"2023-11-20T10:29:18Z","file_id":"14571"},{"success":1,"date_created":"2023-11-20T10:44:39Z","content_type":"application/zip","access_level":"open_access","creator":"fschur","relation":"main_file","file_name":"Figure5.zip","checksum":"bdeb232dc94d0c22a3f7e0d18189ce89","file_size":5154614201,"date_updated":"2023-11-20T10:44:39Z","file_id":"14572"},{"success":1,"date_created":"2023-11-20T10:46:00Z","content_type":"application/zip","access_level":"open_access","creator":"fschur","relation":"main_file","file_name":"SupplementaryFigure7.zip","checksum":"83aee17d621a05d865f68f39c8892d27","file_size":1277893286,"date_updated":"2023-11-20T10:46:00Z","file_id":"14573"},{"date_updated":"2023-11-20T10:46:08Z","file_id":"14574","file_size":228485124,"checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","file_name":"SupplementaryFigure9.zip","relation":"main_file","access_level":"open_access","creator":"fschur","content_type":"application/zip","date_created":"2023-11-20T10:46:08Z","success":1},{"date_created":"2023-11-20T10:46:32Z","success":1,"content_type":"application/zip","access_level":"open_access","creator":"fschur","relation":"main_file","checksum":"4f3644e5feabe4824486d56885bb79fe","file_name":"SupplementaryFigure10.zip","file_size":1226788198,"file_id":"14575","date_updated":"2023-11-20T10:46:32Z"},{"content_type":"application/zip","date_created":"2023-11-20T10:46:17Z","success":1,"relation":"main_file","access_level":"open_access","creator":"fschur","file_size":277577131,"checksum":"96167f722ed0ca78e30681cd1573b9d7","file_name":"SupplementaryFigure11.zip","file_id":"14576","date_updated":"2023-11-20T10:46:17Z"},{"file_size":591483468,"file_name":"SupplementaryFigure15.zip","checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","file_id":"14577","date_updated":"2023-11-20T10:46:29Z","content_type":"application/zip","success":1,"date_created":"2023-11-20T10:46:29Z","relation":"main_file","access_level":"open_access","creator":"fschur"},{"date_updated":"2023-11-20T10:47:00Z","file_id":"14578","checksum":"4d437c04fdb3c1e699618063c4bd21c3","file_name":"SupplementaryFigure17.zip","file_size":1709528579,"creator":"fschur","access_level":"open_access","relation":"main_file","date_created":"2023-11-20T10:47:00Z","success":1,"content_type":"application/zip"},{"file_id":"14581","date_updated":"2023-11-20T11:26:36Z","file_size":1920765280,"checksum":"967b5378a4f16c43f490eae328afe50e","file_name":"SupplementaryFigure4.zip","relation":"main_file","access_level":"open_access","creator":"fschur","content_type":"application/zip","date_created":"2023-11-20T11:26:36Z","success":1},{"file_id":"14583","date_updated":"2023-11-20T11:38:12Z","file_size":3013566196,"checksum":"11899986cf0b471d258fe168ee33a3ea","file_name":"Figure1_partA.zip","relation":"main_file","creator":"fschur","access_level":"open_access","content_type":"application/zip","date_created":"2023-11-20T11:38:12Z","success":1},{"file_name":"Figure1_partB.zip","checksum":"c452afe1ab506d58d32e601d5b3878bb","file_size":3250260203,"file_id":"14584","date_updated":"2023-11-20T11:43:23Z","success":1,"date_created":"2023-11-20T11:43:23Z","content_type":"application/zip","access_level":"open_access","creator":"fschur","relation":"main_file"},{"date_updated":"2023-11-20T11:49:58Z","file_id":"14585","file_size":1460,"file_name":"ReadMe.rtf","checksum":"223c98eceecbe65dd268f4f363a620d8","relation":"main_file","creator":"fschur","access_level":"open_access","content_type":"text/rtf","success":1,"date_created":"2023-11-20T11:49:58Z"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","date_published":"2023-11-21T00:00:00Z","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","first_name":"Florian KM"}],"article_processing_charge":"No","related_material":{"record":[{"id":"12334","relation":"used_in_publication","status":"public"}]},"doi":"10.15479/AT:ISTA:14562","date_updated":"2023-11-21T08:05:34Z","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"file_date_updated":"2023-11-20T11:49:58Z"},{"date_created":"2023-11-20T09:18:21Z","oa_version":"Published Version","publisher":"American Geophysical Union","publication":"Journal of Advances in Modeling Earth Systems","department":[{"_id":"CaMu"}],"title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","abstract":[{"lang":"eng","text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized."}],"year":"2023","has_accepted_license":"1","_id":"14564","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":15,"publication_identifier":{"eissn":["1942-2466"]},"citation":{"ieee":"B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11. American Geophysical Union, 2023.","chicago":"Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2022ms003391\">https://doi.org/10.1029/2022ms003391</a>.","apa":"Khouider, B., GOSWAMI, B. B., Phani, R., &#38; Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. <i>Journal of Advances in Modeling Earth Systems</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2022ms003391\">https://doi.org/10.1029/2022ms003391</a>","ama":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. <i>Journal of Advances in Modeling Earth Systems</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>","mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2022ms003391\">10.1029/2022ms003391</a>.","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023)."},"issue":"11","article_type":"original","acknowledgement":"The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript.","oa":1,"status":"public","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_number":"e2022MS003391","file_date_updated":"2023-11-20T11:29:16Z","quality_controlled":"1","keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"scopus_import":"1","article_processing_charge":"Yes","date_updated":"2023-11-28T12:04:42Z","doi":"10.1029/2022ms003391","date_published":"2023-11-01T00:00:00Z","author":[{"last_name":"Khouider","first_name":"B.","full_name":"Khouider, B."},{"full_name":"GOSWAMI, BIDYUT B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"BIDYUT B","orcid":"0000-0001-8602-3083","last_name":"GOSWAMI"},{"last_name":"Phani","first_name":"R.","full_name":"Phani, R."},{"full_name":"Majda, A. J.","last_name":"Majda","first_name":"A. J."}],"file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","content_type":"application/pdf","success":1,"date_created":"2023-11-20T11:29:16Z","file_id":"14582","date_updated":"2023-11-20T11:29:16Z","file_size":6435697,"file_name":"2023_JAMES_Khoulder.pdf","checksum":"e30329dd985559de0ddc7021ca7382b4"}],"publication_status":"published","intvolume":"        15","month":"11","language":[{"iso":"eng"}],"ddc":["550"],"day":"01"},{"status":"public","oa":1,"ddc":["570"],"day":"11","citation":{"ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>","short":"W. Wetzel, (2023).","mla":"Wetzel, William. <i>HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133117\">10.5281/ZENODO.8133117</a>.","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133117\">https://doi.org/10.5281/ZENODO.8133117</a>.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133117\">https://doi.org/10.5281/ZENODO.8133117</a>"},"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133118","open_access":"1"}],"_id":"14579","year":"2023","date_published":"2023-07-11T00:00:00Z","author":[{"full_name":"Wetzel, William","first_name":"William","last_name":"Wetzel"}],"article_processing_charge":"No","date_updated":"2023-11-20T11:17:33Z","doi":"10.5281/ZENODO.8133117","related_material":{"record":[{"id":"14552","relation":"used_in_publication","status":"public"}]},"abstract":[{"lang":"eng","text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n"}],"title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","department":[{"_id":"NiBa"}],"publisher":"Zenodo","date_created":"2023-11-20T11:07:45Z","oa_version":"Published Version"},{"file_date_updated":"2023-11-29T09:28:30Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"author":[{"id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice","last_name":"Marveggio","first_name":"Alice"}],"date_published":"2023-11-21T00:00:00Z","article_processing_charge":"No","doi":"10.15479/at:ista:14587","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11842"},{"id":"14597","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-11-30T13:25:03Z","degree_awarded":"PhD","file":[{"relation":"main_file","access_level":"open_access","creator":"amarvegg","content_type":"application/pdf","success":1,"date_created":"2023-11-29T09:09:31Z","file_id":"14626","date_updated":"2023-11-29T09:09:31Z","file_size":2881100,"file_name":"thesis_Marveggio.pdf","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4"},{"file_id":"14627","date_updated":"2023-11-29T09:28:30Z","file_name":"Thesis_Marveggio.zip","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","file_size":10189696,"access_level":"open_access","creator":"amarvegg","relation":"source_file","date_created":"2023-11-29T09:10:19Z","content_type":"application/zip"}],"publication_status":"published","ddc":["515"],"day":"21","month":"11","project":[{"call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","publisher":"Institute of Science and Technology Austria","date_created":"2023-11-21T11:41:05Z","ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"page":"228","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","_id":"14587","supervisor":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"}],"has_accepted_license":"1","year":"2023","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","oa":1,"status":"public","citation":{"short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","mla":"Marveggio, Alice. <i>Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>.","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>","apa":"Marveggio, A. (2023). <i>Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023."},"publication_identifier":{"issn":["2663 - 337X"]}},{"citation":{"ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, <a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. .","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>.","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>"},"month":"10","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"status":"public","oa":1,"day":"10","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2"}],"_id":"14591","year":"2023","publication_status":"submitted","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"preprint","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"author":[{"full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson"},{"last_name":"Nagel","first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"last_name":"Hlavata","first_name":"Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria"},{"full_name":"Isono, Erika","last_name":"Isono","first_name":"Erika"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"date_published":"2023-10-10T00:00:00Z","article_processing_charge":"No","related_material":{"record":[{"id":"14510","relation":"dissertation_contains","status":"public"}]},"doi":"10.1101/2023.10.09.561523","date_updated":"2023-12-01T13:51:06Z","date_created":"2023-11-22T10:17:49Z","ec_funded":1,"oa_version":"Preprint","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication":"bioRxiv","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}]},{"publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2023-11-28T08:39:06Z","success":1,"file_id":"14620","date_updated":"2023-11-28T08:39:06Z","file_size":6276059,"checksum":"f668ee0d07096eef81159d05bc27aabc","file_name":"2023_JourChemicalPhysics_Reinhardt.pdf"}],"intvolume":"       159","day":"14","ddc":["530","540"],"language":[{"iso":"eng"}],"month":"11","article_number":"184110","file_date_updated":"2023-11-28T08:39:06Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-11-28T08:39:23Z","doi":"10.1063/5.0173341","related_material":{"record":[{"id":"14619","relation":"research_data","status":"public"}]},"article_processing_charge":"Yes (in subscription journal)","date_published":"2023-11-14T00:00:00Z","author":[{"full_name":"Reinhardt, Aleks","last_name":"Reinhardt","first_name":"Aleks"},{"last_name":"Chew","first_name":"Pin Yu","full_name":"Chew, Pin Yu"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing"}],"quality_controlled":"1","scopus_import":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":159,"year":"2023","has_accepted_license":"1","_id":"14603","article_type":"original","external_id":{"arxiv":["2308.10886"]},"issue":"18","status":"public","acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","oa":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"citation":{"ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” <i>Journal of Chemical Physics</i>, vol. 159, no. 18. AIP Publishing, 2023.","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>.","apa":"Reinhardt, A., Chew, P. Y., &#38; Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. 2023;159(18). doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>","ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>."},"publisher":"AIP Publishing","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","department":[{"_id":"BiCh"}],"publication":"Journal of Chemical Physics","oa_version":"Published Version","date_created":"2023-11-26T23:00:54Z","arxiv":1,"abstract":[{"lang":"eng","text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances."}]},{"title":"The X chromosome of insects likely predates the origin of class Insecta","department":[{"_id":"BeVi"}],"publication":"Evolution","publisher":"Oxford University Press","oa_version":"Published Version","date_created":"2023-11-26T23:00:54Z","abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"page":"2504-2511","volume":77,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14604","has_accepted_license":"1","year":"2023","acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","oa":1,"status":"public","external_id":{"pmid":["37738212"]},"article_type":"original","issue":"11","citation":{"apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” <i>Evolution</i>, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. 2023;77(11):2504-2511. doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>"},"publication_identifier":{"eissn":["1558-5646"]},"file_date_updated":"2023-11-28T08:12:15Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"date_published":"2023-11-02T00:00:00Z","doi":"10.1093/evolut/qpad169","date_updated":"2023-11-28T08:25:28Z","related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/veryoldx"}],"record":[{"id":"14616","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"14617"}]},"article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","quality_controlled":"1","intvolume":"        77","publication_status":"published","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2023-11-28T08:12:15Z","date_updated":"2023-11-28T08:12:15Z","file_id":"14618","file_size":1399102,"file_name":"2023_Evolution_Toups.pdf","checksum":"b66dc10edae92d38918d534e64dda77c"}],"pmid":1,"day":"02","ddc":["570"],"language":[{"iso":"eng"}],"month":"11"}]