[{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/D4CC02609H"}],"year":"2024","intvolume":"        60","OA_place":"publisher","language":[{"iso":"eng"}],"external_id":{"pmid":["39118590"]},"oa":1,"date_created":"2025-12-09T14:23:00Z","license":"https://creativecommons.org/licenses/by-nc/3.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","OA_type":"hybrid","day":"02","publisher":"Royal Society of Chemistry","doi":"10.1039/d4cc02609h","publication":"Chemical Communications","extern":"1","quality_controlled":"1","pmid":1,"page":"9254-9257","publication_status":"published","date_published":"2024-08-02T00:00:00Z","author":[{"last_name":"Botlik","full_name":"Botlik, Bence B.","first_name":"Bence B."},{"last_name":"Finkelstein","full_name":"Finkelstein, Patrick","first_name":"Patrick"},{"last_name":"Paschke","full_name":"Paschke, Ann-Sophie K.","first_name":"Ann-Sophie K."},{"id":"51d862e9-36ee-11f0-86d3-8534c85a5496","first_name":"Julia","last_name":"Reisenbauer","full_name":"Reisenbauer, Julia"},{"first_name":"Bill","last_name":"Morandi","full_name":"Morandi, Bill"}],"title":"Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"has_accepted_license":"1","oa_version":"Published Version","volume":60,"month":"08","abstract":[{"lang":"eng","text":"We report the utilisation of an iodine(III) reagent to access α,β-unsaturated carbonyls from the corresponding silyl enol ethers and enol phosphates. The transformation can also be carried out in one pot, directly dehydrogenating carbonyls."}],"issue":"69","date_updated":"2025-12-16T11:19:43Z","article_type":"original","status":"public","_id":"20757","article_processing_charge":"No","citation":{"short":"B.B. Botlik, P. Finkelstein, A.-S.K. Paschke, J. Reisenbauer, B. Morandi, Chemical Communications 60 (2024) 9254–9257.","ista":"Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. 2024. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. 60(69), 9254–9257.","chicago":"Botlik, Bence B., Patrick Finkelstein, Ann-Sophie K. Paschke, Julia Reisenbauer, and Bill Morandi. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d4cc02609h\">https://doi.org/10.1039/d4cc02609h</a>.","ieee":"B. B. Botlik, P. Finkelstein, A.-S. K. Paschke, J. Reisenbauer, and B. Morandi, “Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent,” <i>Chemical Communications</i>, vol. 60, no. 69. Royal Society of Chemistry, pp. 9254–9257, 2024.","mla":"Botlik, Bence B., et al. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” <i>Chemical Communications</i>, vol. 60, no. 69, Royal Society of Chemistry, 2024, pp. 9254–57, doi:<a href=\"https://doi.org/10.1039/d4cc02609h\">10.1039/d4cc02609h</a>.","ama":"Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. <i>Chemical Communications</i>. 2024;60(69):9254-9257. doi:<a href=\"https://doi.org/10.1039/d4cc02609h\">10.1039/d4cc02609h</a>","apa":"Botlik, B. B., Finkelstein, P., Paschke, A.-S. K., Reisenbauer, J., &#38; Morandi, B. (2024). Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4cc02609h\">https://doi.org/10.1039/d4cc02609h</a>"},"type":"journal_article","publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]}},{"date_updated":"2025-12-15T10:21:56Z","issue":"1","abstract":[{"lang":"eng","text":"Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes."}],"volume":44,"month":"01","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","has_accepted_license":"1","citation":{"ama":"Panska L, Nedvedova S, Vacek V, et al. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. <i>Bioscience Reports</i>. 2024;44(1). doi:<a href=\"https://doi.org/10.1042/bsr20230502\">10.1042/bsr20230502</a>","apa":"Panska, L., Nedvedova, S., Vacek, V., Krivska, D., Konecny, L., Knop, F., … Dvorak, J. (2024). Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. <i>Bioscience Reports</i>. Portland Press. <a href=\"https://doi.org/10.1042/bsr20230502\">https://doi.org/10.1042/bsr20230502</a>","ista":"Panska L, Nedvedova S, Vacek V, Krivska D, Konecny L, Knop F, Kutil Z, Skultetyova L, Leontovyc A, Ulrychova L, Sakanari J, Asahina M, Barinka C, Macurkova M, Dvorak J. 2024. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. 44(1), BSR20230502.","short":"L. Panska, S. Nedvedova, V. Vacek, D. Krivska, L. Konecny, F. Knop, Z. Kutil, L. Skultetyova, A. Leontovyc, L. Ulrychova, J. Sakanari, M. Asahina, C. Barinka, M. Macurkova, J. Dvorak, Bioscience Reports 44 (2024).","mla":"Panska, Lucie, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” <i>Bioscience Reports</i>, vol. 44, no. 1, BSR20230502, Portland Press, 2024, doi:<a href=\"https://doi.org/10.1042/bsr20230502\">10.1042/bsr20230502</a>.","chicago":"Panska, Lucie, Stepanka Nedvedova, Vojtech Vacek, Daniela Krivska, Lukas Konecny, Filip Knop, Zsofia Kutil, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” <i>Bioscience Reports</i>. Portland Press, 2024. <a href=\"https://doi.org/10.1042/bsr20230502\">https://doi.org/10.1042/bsr20230502</a>.","ieee":"L. Panska <i>et al.</i>, “Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans,” <i>Bioscience Reports</i>, vol. 44, no. 1. Portland Press, 2024."},"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1573-4935"],"issn":["0144-8463"]},"type":"journal_article","status":"public","_id":"20807","publication_status":"published","publication":"Bioscience Reports","extern":"1","pmid":1,"quality_controlled":"1","title":"Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans","author":[{"last_name":"Panska","full_name":"Panska, Lucie","first_name":"Lucie"},{"full_name":"Nedvedova, Stepanka","last_name":"Nedvedova","first_name":"Stepanka"},{"first_name":"Vojtech","last_name":"Vacek","full_name":"Vacek, Vojtech"},{"last_name":"Krivska","full_name":"Krivska, Daniela","first_name":"Daniela"},{"first_name":"Lukas","last_name":"Konecny","full_name":"Konecny, Lukas"},{"first_name":"Filip","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","full_name":"Knop, Filip","orcid":"0000-0002-3845-3465","last_name":"Knop"},{"full_name":"Kutil, Zsofia","last_name":"Kutil","first_name":"Zsofia"},{"first_name":"Lubica","last_name":"Skultetyova","full_name":"Skultetyova, Lubica"},{"first_name":"Adrian","last_name":"Leontovyc","full_name":"Leontovyc, Adrian"},{"last_name":"Ulrychova","full_name":"Ulrychova, Lenka","first_name":"Lenka"},{"first_name":"Judy","last_name":"Sakanari","full_name":"Sakanari, Judy"},{"first_name":"Masako","last_name":"Asahina","full_name":"Asahina, Masako"},{"first_name":"Cyril","full_name":"Barinka, Cyril","last_name":"Barinka"},{"last_name":"Macurkova","full_name":"Macurkova, Marie","first_name":"Marie"},{"first_name":"Jan","full_name":"Dvorak, Jan","last_name":"Dvorak"}],"date_published":"2024-01-12T00:00:00Z","article_number":"BSR20230502","scopus_import":"1","ddc":["570"],"publisher":"Portland Press","doi":"10.1042/bsr20230502","day":"12","OA_type":"hybrid","intvolume":"        44","year":"2024","main_file_link":[{"url":"https://doi.org/10.1042/BSR20230502","open_access":"1"}],"oa":1,"date_created":"2025-12-12T09:03:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","external_id":{"pmid":["38108122 "]},"language":[{"iso":"eng"}]},{"oa_version":"Published Version","date_updated":"2025-12-15T10:26:56Z","month":"07","abstract":[{"lang":"eng","text":"During Caenorhabditis elegans development, multiple cells migrate long distances or extend processes to reach their final position and/or attain proper shape. The Wnt signalling pathway stands out as one of the major coordinators of cell migration or cell outgrowth along the anterior-posterior body axis. The outcome of Wnt signalling is fine-tuned by various mechanisms including endocytosis. In this study, we show that SEL-5, the C. elegans orthologue of mammalian AP2-associated kinase AAK1, acts together with the retromer complex as a positive regulator of EGL-20/Wnt signalling during the migration of QL neuroblast daughter cells. At the same time, SEL-5 in cooperation with the retromer complex is also required during excretory canal cell outgrowth. Importantly, SEL-5 kinase activity is not required for its role in neuronal migration or excretory cell outgrowth, and neither of these processes is dependent on DPY-23/AP2M1 phosphorylation. We further establish that the Wnt proteins CWN-1 and CWN-2, together with the Frizzled receptor CFZ-2, positively regulate excretory cell outgrowth, while LIN-44/Wnt and LIN-17/Frizzled together generate a stop signal inhibiting its extension."}],"volume":13,"article_type":"original","_id":"20808","status":"public","citation":{"apa":"Knop, F., Zounarová, A., Šabata, V., Middelkoop, T. C., &#38; Macůrková, M. (2024). Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91054\">https://doi.org/10.7554/elife.91054</a>","ama":"Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.91054\">10.7554/elife.91054</a>","ieee":"F. Knop, A. Zounarová, V. Šabata, T. C. Middelkoop, and M. Macůrková, “Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","chicago":"Knop, Filip, Apolena Zounarová, Vojtěch Šabata, Teije Corneel Middelkoop, and Marie Macůrková. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91054\">https://doi.org/10.7554/elife.91054</a>.","mla":"Knop, Filip, et al. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” <i>ELife</i>, vol. 13, e91054, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91054\">10.7554/elife.91054</a>.","short":"F. Knop, A. Zounarová, V. Šabata, T.C. Middelkoop, M. Macůrková, ELife 13 (2024).","ista":"Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. 2024. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. eLife. 13, e91054."},"article_processing_charge":"Yes","publication_identifier":{"eissn":["2050-084X"]},"type":"journal_article","publication":"eLife","extern":"1","pmid":1,"quality_controlled":"1","publication_status":"published","author":[{"first_name":"Filip","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","full_name":"Knop, Filip","orcid":"0000-0002-3845-3465","last_name":"Knop"},{"first_name":"Apolena","last_name":"Zounarová","full_name":"Zounarová, Apolena"},{"first_name":"Vojtěch","full_name":"Šabata, Vojtěch","last_name":"Šabata"},{"last_name":"Middelkoop","full_name":"Middelkoop, Teije Corneel","first_name":"Teije Corneel"},{"first_name":"Marie","last_name":"Macůrková","full_name":"Macůrková, Marie"}],"date_published":"2024-07-19T00:00:00Z","article_number":"e91054","title":"Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity","scopus_import":"1","DOAJ_listed":"1","OA_type":"gold","day":"19","publisher":"eLife Sciences Publications","doi":"10.7554/elife.91054","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/elife.91054"}],"intvolume":"        13","year":"2024","OA_place":"publisher","external_id":{"pmid":["39028260"]},"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-12T09:06:31Z"},{"title":"Divergence of separated nets with respect to displacement equivalence","article_number":"15","date_published":"2024-02-01T00:00:00Z","author":[{"last_name":"Dymond","full_name":"Dymond, Michael","first_name":"Michael"},{"id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","first_name":"Vojtech","orcid":"0000-0002-2512-8698","last_name":"Kaluza","full_name":"Kaluza, Vojtech"}],"publication_status":"published","quality_controlled":"1","pmid":1,"file":[{"relation":"main_file","success":1,"creator":"dernst","checksum":"9418534ac2f3d6f1f091a8b8ccaed01e","date_updated":"2024-07-16T10:14:13Z","date_created":"2024-07-16T10:14:13Z","file_size":540981,"file_name":"2024_GeometriaeDedicata_Dymond.pdf","file_id":"17257","content_type":"application/pdf","access_level":"open_access"}],"publication":"Geometriae Dedicata","type":"journal_article","publication_identifier":{"eissn":["1572-9168"],"issn":["0046-5755"]},"article_processing_charge":"Yes (via OA deal)","citation":{"short":"M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024).","ista":"Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15.","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” <i>Geometriae Dedicata</i>, vol. 218. Springer Nature, 2024.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>.","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>, vol. 218, 15, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. 2024;218. doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>","apa":"Dymond, M., &#38; Kaluza, V. (2024). Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>"},"_id":"9651","status":"public","article_type":"original","abstract":[{"lang":"eng","text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence."}],"volume":218,"month":"02","date_updated":"2025-04-23T07:37:26Z","has_accepted_license":"1","oa_version":"Published Version","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_created":"2021-07-14T07:01:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2024-07-16T10:14:13Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2102.13046"],"pmid":["38021107"],"isi":["001105681500001"]},"OA_place":"publisher","corr_author":"1","year":"2024","department":[{"_id":"UlWa"}],"intvolume":"       218","arxiv":1,"doi":"10.1007/s10711-023-00862-3","publisher":"Springer Nature","OA_type":"hybrid","day":"01","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","ddc":["510"],"scopus_import":"1"},{"project":[{"name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"},{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"year":"2024","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"intvolume":"        15","date_created":"2024-07-04T11:40:45Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2024-08-05T08:38:01Z","oa":1,"external_id":{"arxiv":["2403.16774"],"isi":["001281271000022"],"pmid":["39080279"]},"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","ddc":["530"],"acknowledgement":"We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support.","scopus_import":"1","doi":"10.1038/s41467-024-50763-6","arxiv":1,"publisher":"Springer Nature","day":"30","OA_type":"gold","DOAJ_listed":"1","APC_amount":"6828 EUR","publication_status":"published","pmid":1,"quality_controlled":"1","file":[{"file_id":"17388","access_level":"open_access","file_name":"2024_NatureComm_Sagi.pdf","content_type":"application/pdf","date_created":"2024-08-05T08:38:01Z","file_size":1928001,"date_updated":"2024-08-05T08:38:01Z","checksum":"ddf5361dcb6c543e2cea818501c09910","success":1,"relation":"main_file","creator":"dernst"}],"publication":"Nature Communications","title":"A gate tunable transmon qubit in planar Ge","author":[{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro","orcid":"0000-0002-2968-611X","last_name":"Crippa","full_name":"Crippa, Alessandro"},{"full_name":"Valentini, Marco","last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","orcid":"0009-0003-9037-8831","last_name":"Janik","full_name":"Janik, Marian"},{"first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","full_name":"Baghumyan, Levon","last_name":"Baghumyan"},{"first_name":"Giorgio","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","full_name":"Fabris, Giorgio","last_name":"Fabris"},{"first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","full_name":"Kapoor, Lucky","last_name":"Kapoor","orcid":"0000-0001-8319-2148"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefano","full_name":"Calcaterra, Stefano","last_name":"Calcaterra"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"date_published":"2024-07-30T00:00:00Z","article_number":"6400","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-024-53910-1"}],"record":[{"relation":"research_data","id":"17196","status":"public"},{"relation":"dissertation_contains","status":"public","id":"18076"}]},"article_type":"original","date_updated":"2026-04-07T13:01:55Z","month":"07","volume":15,"abstract":[{"text":"Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.","lang":"eng"}],"isi":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","citation":{"mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>, vol. 15, 6400, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>.","chicago":"Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>.","ieee":"O. Sagi <i>et al.</i>, “A gate tunable transmon qubit in planar Ge,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ista":"Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400.","short":"O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>","ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>"},"article_processing_charge":"Yes","_id":"17202","status":"public"},{"status":"public","_id":"17203","type":"journal_article","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Hafner, C., Ly, M., &#38; Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. <i>Transactions on Graphics</i>. Denver, Colorado: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658194\">https://doi.org/10.1145/3658194</a>","ama":"Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. <i>Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658194\">10.1145/3658194</a>","ieee":"C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” <i>Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","chicago":"Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” <i>Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658194\">https://doi.org/10.1145/3658194</a>.","mla":"Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” <i>Transactions on Graphics</i>, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658194\">10.1145/3658194</a>.","short":"C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).","ista":"Hafner C, Ly M, Wojtan C. 2024. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 43(4), 78."},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"article_type":"original","keyword":["Topology Optimization","Mass Moments","Computational Geometry"],"month":"07","volume":43,"abstract":[{"lang":"eng","text":"The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found.\r\n\r\nIn this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain."}],"issue":"4","date_updated":"2025-09-08T08:29:09Z","date_published":"2024-07-01T00:00:00Z","article_number":"78","author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"},{"last_name":"Ly","full_name":"Ly, Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"Mickaël"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"title":"Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments","conference":{"end_date":"2024-08-01","location":"Denver, Colorado","start_date":"2024-07-28"},"quality_controlled":"1","publication":"Transactions on Graphics","file":[{"date_created":"2024-07-05T12:05:17Z","file_size":7225150,"access_level":"open_access","content_type":"application/pdf","file_name":"sif-final.pdf","file_id":"17204","success":1,"checksum":"0dc9f5a6422b8a49a79026900f349ee5","creator":"chafner","relation":"main_file","date_updated":"2024-07-05T12:05:17Z"},{"content_type":"application/pdf","access_level":"open_access","file_name":"sif-supp-final.pdf","file_id":"17205","file_size":397262,"date_created":"2024-07-05T12:06:03Z","date_updated":"2024-07-05T12:06:03Z","relation":"supplementary_material","checksum":"cde433c6a40688d5f1187fb5721f6f94","creator":"chafner"},{"title":"Submission Video","file_size":170001305,"date_created":"2024-07-17T09:29:13Z","access_level":"open_access","content_type":"video/mp4","file_name":"sif-video-final.mp4","file_id":"17276","checksum":"c0457a09c2ab9a1c2935c995dcc84907","relation":"supplementary_material","creator":"chafner","date_updated":"2024-07-17T09:29:13Z"}],"publication_status":"published","day":"01","doi":"10.1145/3658194","publisher":"Association for Computing Machinery","ddc":["516"],"acknowledgement":"We thank Gianmarco Cherchi for his help in tailoring the Mesh Booleans code for this project, Stefan Jeschke for his help with the photographs, Malina Strugaru and Aleksei Kalinov for their help with the samples, and the anonymous reviewers as well as the members of the ISTA Visual Computing Group for their feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001289270900045"]},"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-05T12:08:57Z","oa":1,"file_date_updated":"2024-07-17T09:29:13Z","intvolume":"        43","year":"2024","department":[{"_id":"ChWo"}],"project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}]},{"article_type":"letter_note","volume":37,"month":"06","issue":"6","date_updated":"2026-06-18T17:53:35Z","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","publication_identifier":{"eissn":["1420-9101"]},"article_processing_charge":"No","citation":{"ama":"Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of evolutionary biology</i>. 2024;37(6):579-587. doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>","apa":"Fouqueau, L., &#38; Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587.","ista":"Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.","chicago":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>.","ieee":"L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” <i>Journal of evolutionary biology</i>, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.","mla":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>."},"_id":"17207","status":"public","publication_status":"published","page":"579-587","quality_controlled":"1","pmid":1,"publication":"Journal of evolutionary biology","title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","date_published":"2024-06-28T00:00:00Z","author":[{"last_name":"Fouqueau","orcid":"0000-0003-0371-9339","full_name":"Fouqueau, Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise"},{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova"}],"acknowledgement":"This research was funded by the Austrian Science Fund (FWF), project doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896 and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton for their insightful comments on the earlier drafts, and to John Carchrae for his valuable contribution in refining phrasing and enhancing clarity. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","ddc":["570"],"scopus_import":"1","doi":"10.1093/jeb/voae067","publisher":"Oxford University Press","day":"28","year":"2024","intvolume":"        37","department":[{"_id":"NiBa"}],"project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jeb/voae067"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-07-07T22:01:04Z","oa":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["38941551"],"isi":["001258359900001"]}},{"ddc":["539"],"doi":"10.15479/at:ista:17208","publisher":"Institute of Science and Technology Austria","day":"09","alternative_title":["ISTA Thesis"],"ec_funded":1,"year":"2024","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"project":[{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"date_created":"2024-07-09T09:14:24Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","oa":1,"file_date_updated":"2024-07-17T09:23:24Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"related_material":{"record":[{"id":"10545","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"10067","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17222","status":"public"},{"id":"13125","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11471"}]},"abstract":[{"lang":"eng","text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization.  We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration."}],"month":"07","date_updated":"2026-04-07T12:43:22Z","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","citation":{"mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>"},"_id":"17208","supervisor":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"}],"status":"public","page":"133","publication_status":"published","file":[{"date_created":"2024-07-09T09:21:44Z","file_size":"14218691","access_level":"closed","file_id":"17212","file_name":"Raimel_Thesis-Final.zip","content_type":"application/zip","relation":"source_file","creator":"rmedinar","checksum":"6f45273d04f4418bc2adc018baed0525","date_updated":"2024-07-10T11:34:09Z"},{"access_level":"open_access","file_id":"17275","content_type":"application/pdf","file_name":"Raimel_Thesis-20_pdfa.pdf","date_created":"2024-07-17T09:23:24Z","file_size":11253627,"date_updated":"2024-07-17T09:23:24Z","checksum":"6724a95bec772dbabc0111b9f08a805e","success":1,"creator":"rmedinar","relation":"main_file"}],"title":"Exploring the optimization landscape of variational quantum algorithms","date_published":"2024-07-09T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869","last_name":"Medina Ramos"}]},{"file_date_updated":"2024-07-10T11:03:58Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-10T11:06:20Z","corr_author":"1","external_id":{"isi":["001282218200091"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"year":"2024","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","doi":"10.1145/3641519.3657485","day":"01","scopus_import":"1","acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","ddc":["621","531","006"],"conference":{"end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28","location":"Denver, United States"},"title":"Primal-dual non-smooth friction for rigid body animation","author":[{"id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","first_name":"Yi-Lu","last_name":"Chen","full_name":"Chen, Yi-Lu"},{"full_name":"Ly, Mickaël","last_name":"Ly","first_name":"Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"date_published":"2024-07-01T00:00:00Z","publication_status":"published","file":[{"file_size":47309472,"date_created":"2024-07-10T11:03:14Z","file_id":"17215","file_name":"sig24_friction_authors.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"yichen","relation":"main_file","checksum":"b8b203ed09e3995ba0d7e6a76288663a","date_updated":"2024-07-10T11:03:14Z"},{"file_size":10518286,"date_created":"2024-07-10T11:03:12Z","file_name":"sig24_friction_supplementary.pdf","access_level":"open_access","file_id":"17216","content_type":"application/pdf","creator":"yichen","checksum":"89d81b397b4b6469d828808a68b70820","success":1,"relation":"main_file","date_updated":"2024-07-10T11:03:12Z"},{"file_size":71789192,"date_created":"2024-07-10T11:03:51Z","content_type":"video/mp4","access_level":"open_access","file_name":"friction_paper_extra_video_finished.mp4","file_id":"17217","checksum":"7123deed34a5456810e7b5336a31c657","creator":"yichen","relation":"main_file","success":1,"date_updated":"2024-07-10T11:03:51Z"},{"file_size":280610763,"date_created":"2024-07-10T11:03:58Z","access_level":"open_access","file_name":"friction_paper_video_finished.mp4","content_type":"video/mp4","file_id":"17218","checksum":"e606fc1ae8f2610ce3b4421566800b45","relation":"main_file","creator":"yichen","success":1,"date_updated":"2024-07-10T11:03:58Z"}],"publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","quality_controlled":"1","citation":{"apa":"Chen, Y.-L., Ly, M., &#38; Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Denver, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Denver, United States, 2024.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>.","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference."},"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"isbn":["9798400705250"]},"type":"conference","status":"public","_id":"17214","date_updated":"2025-09-08T08:54:38Z","month":"07","abstract":[{"text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.","lang":"eng"}],"keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"isi":1,"oa_version":"Published Version","has_accepted_license":"1"},{"day":"01","OA_type":"hybrid","publisher":"Association for Computing Machinery","doi":"10.1145/3658223","scopus_import":"1","acknowledgement":"Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses.  This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","ddc":["004"],"OA_place":"publisher","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001289270900021"]},"oa":1,"file_date_updated":"2025-11-11T09:50:52Z","date_created":"2024-07-10T12:24:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"intvolume":"        43","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"_id":"17219","status":"public","article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., &#38; Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>","ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>.","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>.","ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54.","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024)."},"type":"journal_article","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"abstract":[{"text":"We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.","lang":"eng"}],"volume":43,"month":"07","issue":"4","date_updated":"2026-04-07T13:02:36Z","keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"article_type":"original","related_material":{"record":[{"status":"public","id":"19630","relation":"dissertation_contains"},{"status":"public","id":"18301","relation":"dissertation_contains"}]},"article_number":"54","date_published":"2024-07-01T00:00:00Z","author":[{"first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter","last_name":"Synak"},{"first_name":"Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","full_name":"Kalinov, Aleksei","orcid":"0000-0003-2189-3904","last_name":"Kalinov"},{"first_name":"Irina-Malina","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","full_name":"Strugaru, Irina-Malina","last_name":"Strugaru"},{"first_name":"Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","full_name":"Etemadihaghighi, Arian","last_name":"Etemadihaghighi"},{"first_name":"Huidong","full_name":"Yang, Huidong","last_name":"Yang"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"title":"Multi-material mesh-based surface tracking with implicit topology changes","publication":"ACM Transactions on Graphics","file":[{"access_level":"open_access","file_name":"2024_ACMToG_HeissSynak.pdf","content_type":"application/pdf","file_id":"17317","date_created":"2024-07-23T06:35:15Z","file_size":48763368,"date_updated":"2024-07-23T06:35:15Z","checksum":"1917067d4b52d7729019b03560004e43","success":1,"creator":"dernst","relation":"main_file"},{"access_level":"open_access","file_name":"sdtopofixer_final.mp4","file_id":"17221","content_type":"video/mp4","file_size":48021463,"date_created":"2024-07-10T12:23:44Z","date_updated":"2024-07-10T12:23:44Z","relation":"main_file","checksum":"a4f0e293184bfa034c0c585848806b17","success":1,"creator":"akalinov"},{"relation":"preprint","creator":"akalinov","checksum":"18fc310a78ec91651148c45a8b89fa44","date_updated":"2025-11-11T09:50:52Z","file_size":48639581,"title":"Authors' version of the text","date_created":"2025-11-11T09:50:52Z","file_name":"SuperDuperTopoFixer.pdf","content_type":"application/pdf","file_id":"20633","access_level":"open_access"}],"quality_controlled":"1","publication_status":"published"},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["2405.10125"]},"OA_place":"repository","article_number":"2405.10125","date_published":"2024-05-16T00:00:00Z","author":[{"last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"corr_author":"1","title":"A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm","date_created":"2024-07-10T13:12:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.10125","open_access":"1"}],"publication":"arXiv","department":[{"_id":"MaSe"}],"year":"2024","publication_status":"draft","_id":"17222","day":"16","status":"public","type":"preprint","arxiv":1,"doi":"10.48550/arXiv.2405.10125","article_processing_charge":"No","citation":{"apa":"Medina Ramos, R. A., &#38; Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>","ama":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, 2405.10125, doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>.","ieee":"R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” <i>arXiv</i>. .","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>.","ista":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv, 2405.10125.","short":"R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.)."},"oa_version":"Preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17208"}]},"abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto implement a variational method with $2p$ layers of alternating unitary\r\noperators, optimized by a classical computer to minimize a cost function. While\r\nrigorous performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior at large depths remains less clear, though simulations suggest\r\nexponentially fast convergence for certain problems. In this work, we gain\r\ninsights into the deep QAOA using an analytic expansion of the cost function\r\naround transition states. Transition states are constructed in a recursive\r\nmanner: from the local minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA with $p+1$ layers, which are stationary points characterized\r\nby a unique direction of negative curvature. We construct an analytic estimate\r\nof the negative curvature and the corresponding direction in parameter space at\r\neach transition state. The expansion of the QAOA cost function along the\r\nnegative direction to the quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We provide physical intuition behind the analytic\r\nexpressions for the local curvature and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy of our approximations and reveals that\r\nthe obtained bound and the true value of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study establishes an analytical method for\r\nrecursively studying the QAOA that is applicable in the regime of high circuit\r\ndepth.","lang":"eng"}],"month":"05","date_updated":"2026-04-07T12:43:22Z"},{"day":"20","OA_type":"gold","doi":"10.1016/j.xpro.2024.103168","publisher":"Elsevier","ddc":["570"],"acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["38968076"]},"OA_place":"publisher","corr_author":"1","date_created":"2024-07-14T22:01:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2025-01-09T12:16:53Z","intvolume":"         5","year":"2024","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"status":"public","_id":"17232","type":"journal_article","publication_identifier":{"eissn":["2666-1667"]},"article_processing_charge":"Yes","citation":{"ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>."},"has_accepted_license":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","month":"09","abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"volume":5,"issue":"3","date_updated":"2025-12-30T10:54:12Z","date_published":"2024-09-20T00:00:00Z","article_number":"103168","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","full_name":"Koppensteiner, Peter"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","quality_controlled":"1","pmid":1,"file":[{"file_id":"18810","access_level":"open_access","file_name":"2024_STARProtoc_Cheung2.pdf","content_type":"application/pdf","date_created":"2025-01-09T12:16:53Z","file_size":6445556,"date_updated":"2025-01-09T12:16:53Z","relation":"main_file","creator":"dernst","success":1,"checksum":"464f52ecc6ec92f509552823bb82bf79"}],"publication":"STAR Protocols","APC_amount":"804 EUR","publication_status":"published"},{"ddc":["570"],"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.).","scopus_import":"1","day":"05","doi":"10.21769/BioProtoc.5029","publisher":"Bio-Protocol","year":"2024","department":[{"_id":"MiSi"}],"intvolume":"        14","external_id":{"pmid":["39007160"]},"language":[{"iso":"eng"}],"date_created":"2024-07-14T22:01:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-07-16T06:16:11Z","oa":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_type":"original","issue":"13","date_updated":"2025-03-06T10:28:18Z","abstract":[{"text":"CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene.","lang":"eng"}],"month":"07","volume":14,"status":"public","_id":"17233","publication_identifier":{"eissn":["2331-8325"]},"type":"journal_article","citation":{"ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-protocol</i>. 2024;14(13). doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>","apa":"LI, Z., Huard, J., Bayer, E. M., &#38; Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>","short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024).","ista":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029.","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” <i>Bio-protocol</i>, vol. 14, no. 13. Bio-Protocol, 2024.","chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>. Bio-Protocol, 2024. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>.","mla":"LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>."},"article_processing_charge":"Yes","pmid":1,"quality_controlled":"1","publication":"Bio-protocol","file":[{"checksum":"c8671c0ad483da6407cb16cc3fef1990","creator":"dernst","success":1,"relation":"main_file","date_updated":"2024-07-16T06:16:11Z","date_created":"2024-07-16T06:16:11Z","file_size":2896048,"content_type":"application/pdf","access_level":"open_access","file_id":"17242","file_name":"2024_BioProtocol_Li.pdf"}],"publication_status":"published","author":[{"last_name":"Li","full_name":"Li, Ziqiang","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","first_name":"Ziqiang"},{"last_name":"Huard","full_name":"Huard, Jennifer","first_name":"Jennifer"},{"last_name":"Bayer","full_name":"Bayer, Emmanuelle M.","first_name":"Emmanuelle M."},{"first_name":"Valérie","last_name":"Wattelet-Boyer","full_name":"Wattelet-Boyer, Valérie"}],"article_number":"e5029","date_published":"2024-07-05T00:00:00Z","title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis"},{"author":[{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"first_name":"Joel","full_name":"Leja, Joel","last_name":"Leja"},{"full_name":"De Graaff, Anna","last_name":"De Graaff","first_name":"Anna"},{"full_name":"Brammer, Gabriel B.","last_name":"Brammer","first_name":"Gabriel B."},{"first_name":"Andrea","full_name":"Weibel, Andrea","last_name":"Weibel"},{"last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter","first_name":"Pieter"},{"full_name":"Baggen, Josephine F.W.","last_name":"Baggen","first_name":"Josephine F.W."},{"first_name":"Katherine A.","last_name":"Suess","full_name":"Suess, Katherine A."},{"first_name":"Jenny E.","full_name":"Greene, Jenny E.","last_name":"Greene"},{"full_name":"Bezanson, Rachel","last_name":"Bezanson","first_name":"Rachel"},{"last_name":"Cleri","full_name":"Cleri, Nikko J.","first_name":"Nikko J."},{"first_name":"Michaela","last_name":"Hirschmann","full_name":"Hirschmann, Michaela"},{"last_name":"Labbé","full_name":"Labbé, Ivo","first_name":"Ivo"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"full_name":"Mcconachie, Ian","last_name":"Mcconachie","first_name":"Ian"},{"first_name":"Rohan P.","full_name":"Naidu, Rohan P.","last_name":"Naidu"},{"full_name":"Nelson, Erica","last_name":"Nelson","first_name":"Erica"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"full_name":"Setton, David J.","last_name":"Setton","first_name":"David J."},{"last_name":"Williams","full_name":"Williams, Christina C.","first_name":"Christina C."}],"article_number":"L13","date_published":"2024-07-01T00:00:00Z","title":"RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","file":[{"date_created":"2024-07-16T06:24:29Z","file_size":3273303,"access_level":"open_access","file_name":"2024_AstrophysicalJourn_Wang.pdf","content_type":"application/pdf","file_id":"17243","checksum":"bb1a6725586df12e745d091b5778bb2b","success":1,"creator":"dernst","relation":"main_file","date_updated":"2024-07-16T06:24:29Z"}],"publication":"Astrophysical Journal Letters","quality_controlled":"1","publication_status":"published","_id":"17234","status":"public","citation":{"mla":"Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>.","chicago":"Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel, Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>.","ieee":"B. Wang <i>et al.</i>, “RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1. IOP Publishing, 2024.","ista":"Wang B, Leja J, De Graaff A, Brammer GB, Weibel A, Van Dokkum P, Baggen JFW, Suess KA, Greene JE, Bezanson R, Cleri NJ, Hirschmann M, Labbé I, Matthee JJ, Mcconachie I, Naidu RP, Nelson E, Oesch PA, Setton DJ, Williams CC. 2024. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 969(1), L13.","short":"B. Wang, J. Leja, A. De Graaff, G.B. Brammer, A. Weibel, P. Van Dokkum, J.F.W. Baggen, K.A. Suess, J.E. Greene, R. Bezanson, N.J. Cleri, M. Hirschmann, I. Labbé, J.J. Matthee, I. Mcconachie, R.P. Naidu, E. Nelson, P.A. Oesch, D.J. Setton, C.C. Williams, Astrophysical Journal Letters 969 (2024).","apa":"Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum, P., … Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>","ama":"Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. <i>Astrophysical Journal Letters</i>. 2024;969(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>"},"article_processing_charge":"Yes","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","date_updated":"2025-09-08T08:10:21Z","issue":"1","month":"07","volume":969,"abstract":[{"text":"The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 μm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems.","lang":"eng"}],"article_type":"original","external_id":{"arxiv":["2405.01473"],"isi":["001257903200001"]},"language":[{"iso":"eng"}],"file_date_updated":"2024-07-16T06:24:29Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-14T22:01:11Z","year":"2024","department":[{"_id":"JoMa"}],"intvolume":"       969","DOAJ_listed":"1","day":"01","publisher":"IOP Publishing","doi":"10.3847/2041-8213/ad55f7","arxiv":1,"scopus_import":"1","acknowledgement":"We thank the anonymous referee for the helpful comments. B.W. and J.L. acknowledge support from JWST-GO04233.009-A. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project No. 562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The JWST data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi:10.17909/3a4n-9p88. Computations for this research were performed on the Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information. \r\nFacilities: HST (ACS, WFC3), JWST (NIRCam, NIRSpec). Software: Astropy (Astropy Collaboration et al. 2013, 2018, 2022), dynesty (Speagle 2020), EAzY (Brammer et al. 2008),\r\nemcee (Foreman-Mackey et al. 2013), Matplotlib (Hunter 2007), msaexp (Brammer 2023b), msafit (de Graaff et al. 2024a), NumPy (Harris et al. 2020), Prospector (Johnson et al. 2021), Python-FSPS (Johnson et al. 2023).","ddc":["520"]},{"intvolume":"        12","year":"2024","department":[{"_id":"AnHi"}],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"language":[{"iso":"eng"}],"external_id":{"isi":["001260942200003"]},"oa":1,"file_date_updated":"2024-07-16T06:30:30Z","date_created":"2024-07-14T22:01:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","acknowledgement":"We thank J. A. Sauls for useful discussions. For funding of our research project, we acknowledge the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED, and ECSEL programme 101007322/MatQu. This project has also received funding from Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291 and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish Quantum Flagship project 359284. This work was performed as part of the Research Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934, and 352935). We also acknowledge funding from an internal strategic innovation project of VTT related to the development of quantum computing technologies. This research was supported by the Scientific Service Units of IST Austria through resources provided by Electron Microscopy Facility. J. Senior acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council of Finland (Research Fellowship Project No. 356542).","ddc":["530"],"day":"01","publisher":"AIP Publishing","doi":"10.1063/5.0202851","file":[{"file_size":9408198,"date_created":"2024-07-16T06:30:30Z","file_name":"2024_APLMaterial_Kohopaa.pdf","access_level":"open_access","file_id":"17244","content_type":"application/pdf","checksum":"32a5cdf0ea9c937f806b6039f3219917","relation":"main_file","creator":"dernst","success":1,"date_updated":"2024-07-16T06:30:30Z"}],"publication":"APL Materials","quality_controlled":"1","publication_status":"published","article_number":"071101","date_published":"2024-07-01T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"author":[{"first_name":"Katja","last_name":"Kohopää","full_name":"Kohopää, Katja"},{"first_name":"Alberto","last_name":"Ronzani","full_name":"Ronzani, Alberto"},{"full_name":"Jabdaraghi, Robab Najafi","last_name":"Jabdaraghi","first_name":"Robab Najafi"},{"full_name":"Bera, Arijit","last_name":"Bera","first_name":"Arijit"},{"last_name":"Ribeiro","full_name":"Ribeiro, Mário","first_name":"Mário"},{"full_name":"Hazra, Dibyendu","last_name":"Hazra","first_name":"Dibyendu"},{"last_name":"Senior","orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L"},{"first_name":"Mika","full_name":"Prunnila, Mika","last_name":"Prunnila"},{"full_name":"Govenius, Joonas","last_name":"Govenius","first_name":"Joonas"},{"last_name":"Lehtinen","full_name":"Lehtinen, Janne S.","first_name":"Janne S."},{"full_name":"Kemppinen, Antti","last_name":"Kemppinen","first_name":"Antti"}],"title":"Effect of ion irradiation on superconducting thin films","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","month":"07","volume":12,"abstract":[{"lang":"eng","text":"We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors."}],"date_updated":"2025-09-08T08:10:58Z","issue":"7","article_type":"original","status":"public","_id":"17235","article_processing_charge":"Yes","citation":{"apa":"Kohopää, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra, D., … Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>","ama":"Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. 2024;12(7). doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>","mla":"Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>.","ieee":"K. Kohopää <i>et al.</i>, “Effect of ion irradiation on superconducting thin films,” <i>APL Materials</i>, vol. 12, no. 7. AIP Publishing, 2024.","chicago":"Kohopää, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera, Mário Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>.","ista":"Kohopää K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL, Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation on superconducting thin films. APL Materials. 12(7), 071101.","short":"K. Kohopää, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L. Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12 (2024)."},"type":"journal_article","publication_identifier":{"eissn":["2166-532X"]}},{"date_published":"2024-06-17T00:00:00Z","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"conference":{"end_date":"2024-06-21","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Nantes, France","start_date":"2024-06-17"},"title":"A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut","publication":"Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures","file":[{"date_updated":"2024-07-16T06:38:08Z","checksum":"6ca18ac8508719dbd5d5735f4c991af2","relation":"main_file","success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_name":"2024_SPAA_Kolmogorov.pdf","file_id":"17245","file_size":1116166,"date_created":"2024-07-16T06:38:08Z"}],"quality_controlled":"1","publication_status":"published","page":"403-414","status":"public","_id":"17236","article_processing_charge":"Yes (via OA deal)","citation":{"ama":"Kolmogorov V. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In: <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2024:403-414. doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>","apa":"Kolmogorov, V. (2024). A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 403–414). Nantes, France: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>","ista":"Kolmogorov V. 2024. A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut. Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 403–414.","short":"V. Kolmogorov, in:, Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2024, pp. 403–414.","mla":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2024, pp. 403–14, doi:<a href=\"https://doi.org/10.1145/3626183.3659969\">10.1145/3626183.3659969</a>.","chicago":"Kolmogorov, Vladimir. “A Simpler and Parallelizable O(√log n)-Approximation Algorithm for Sparsest Cut.” In <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 403–14. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3626183.3659969\">https://doi.org/10.1145/3626183.3659969</a>.","ieee":"V. Kolmogorov, “A simpler and parallelizable O(√log n)-approximation algorithm for sparsest cut,” in <i>Proceedings of the 36th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Nantes, France, 2024, pp. 403–414."},"type":"conference","publication_identifier":{"issn":["1548-6109"],"isbn":["9798400704161"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"abstract":[{"text":"Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain \"chaining\" algorithm that combines results of multiple calls to the maxflow algorithm.\r\nWe present an alternative approach that avoids solving the multicommodity flow problem and instead computes \"violating paths\". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors.\r\nWe also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.","lang":"eng"}],"month":"06","date_updated":"2026-01-21T09:46:25Z","related_material":{"record":[{"status":"public","id":"21007","relation":"extended_version"}]},"OA_place":"publisher","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001253331900044"],"arxiv":["2307.00115"]},"oa":1,"file_date_updated":"2024-07-16T06:38:08Z","date_created":"2024-07-14T22:01:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"VlKo"}],"year":"2024","OA_type":"hybrid","day":"17","publisher":"Association for Computing Machinery","arxiv":1,"doi":"10.1145/3626183.3659969","scopus_import":"1","ddc":["510"]},{"arxiv":1,"doi":"10.1093/jeb/voae048","publisher":"Oxford University Press","day":"01","acknowledgement":"This work was funded by the EU project MARFOR Biodiversa/004/2015. L.F. was additionally funded by the Region Bretagne (ARED 2017 REEALG) and the NOMIS Foundation. The project leading to this publication has received funding from the EC2CO (CNRS) fund and from the European FEDER Fund under project 1166-39417.\r\nThis work is especially dedicated to the memory of Gernot Glöckner who contributed to the sequencing of Laminaria digitata genome and passed away in very recent time. The authors thank the ABiMS platform of the Roscoff biological station (http://abims.sb-roscoff.fr) for providing the HPC resources that contributed to the search results reported in this document. We also acknowledge the staff of the “Cluster de calcul intensif HPC” Platform of the OSU Institut Pythéas (Aix-Marseille Université, INSU-CNRS) for providing the computing facilities.","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-07-14T22:01:12Z","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["2404.14003"],"pmid":["38629140"]},"intvolume":"        37","year":"2024","department":[{"_id":"NiBa"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2404.14003"}],"type":"journal_article","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"article_processing_charge":"No","citation":{"chicago":"Reynes, Lauric, Louise Fouqueau, Didier Aurelle, Stephane Mauger, Christophe Destombe, and Myriam Valero. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae048\">https://doi.org/10.1093/jeb/voae048</a>.","ieee":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, and M. Valero, “Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations,” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6. Oxford University Press, pp. 677–692, 2024.","mla":"Reynes, Lauric, et al. “Temporal Genomics Help in Deciphering Neutral and Adaptive Patterns in the Contemporary Evolution of Kelp Populations.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 677–92, doi:<a href=\"https://doi.org/10.1093/jeb/voae048\">10.1093/jeb/voae048</a>.","short":"L. Reynes, L. Fouqueau, D. Aurelle, S. Mauger, C. Destombe, M. Valero, Journal of Evolutionary Biology 37 (2024) 677–692.","ista":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. 2024. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. Journal of Evolutionary Biology. 37(6), 677–692.","apa":"Reynes, L., Fouqueau, L., Aurelle, D., Mauger, S., Destombe, C., &#38; Valero, M. (2024). Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae048\">https://doi.org/10.1093/jeb/voae048</a>","ama":"Reynes L, Fouqueau L, Aurelle D, Mauger S, Destombe C, Valero M. Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations. <i>Journal of Evolutionary Biology</i>. 2024;37(6):677-692. doi:<a href=\"https://doi.org/10.1093/jeb/voae048\">10.1093/jeb/voae048</a>"},"status":"public","_id":"17237","article_type":"original","abstract":[{"lang":"eng","text":"The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change."}],"month":"06","volume":37,"date_updated":"2025-06-04T07:23:23Z","issue":"6","oa_version":"Preprint","title":"Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations","date_published":"2024-06-01T00:00:00Z","author":[{"full_name":"Reynes, Lauric","last_name":"Reynes","first_name":"Lauric"},{"full_name":"Fouqueau, Louise","last_name":"Fouqueau","orcid":"0000-0003-0371-9339","first_name":"Louise","id":"1676e173-8143-11ed-8927-fe165216a93f"},{"first_name":"Didier","full_name":"Aurelle, Didier","last_name":"Aurelle"},{"first_name":"Stephane","full_name":"Mauger, Stephane","last_name":"Mauger"},{"first_name":"Christophe","full_name":"Destombe, Christophe","last_name":"Destombe"},{"first_name":"Myriam","full_name":"Valero, Myriam","last_name":"Valero"}],"publication_status":"published","page":"677-692","quality_controlled":"1","pmid":1,"publication":"Journal of Evolutionary Biology"},{"acknowledgement":"This work was supported by a grant from the ERC, 101055327, “HaplotypeStructure”. I thank Himani Sachdeva, Michal Hledik, Jitka Polechova, and the reviewers for their helpful comments.","ddc":["570"],"scopus_import":"1","doi":"10.1093/jeb/voae052","publisher":"Oxford University Press","day":"01","project":[{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"department":[{"_id":"NiBa"}],"intvolume":"        37","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-14T22:01:12Z","file_date_updated":"2024-07-15T09:45:25Z","oa":1,"external_id":{"isi":["001225323900001"],"pmid":["38683160"]},"language":[{"iso":"eng"}],"corr_author":"1","article_type":"review","issue":"6","date_updated":"2025-09-08T08:08:41Z","month":"06","volume":37,"abstract":[{"lang":"eng","text":"We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace."}],"oa_version":"Published Version","isi":1,"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"type":"journal_article","citation":{"apa":"Barton, N. H. (2024). Limits to species’ range: The tension between local and global adaptation. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae052\">https://doi.org/10.1093/jeb/voae052</a>","ama":"Barton NH. Limits to species’ range: The tension between local and global adaptation. <i>Journal of Evolutionary Biology</i>. 2024;37(6):605-615. doi:<a href=\"https://doi.org/10.1093/jeb/voae052\">10.1093/jeb/voae052</a>","mla":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 605–15, doi:<a href=\"https://doi.org/10.1093/jeb/voae052\">10.1093/jeb/voae052</a>.","chicago":"Barton, Nicholas H. “Limits to Species’ Range: The Tension between Local and Global Adaptation.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae052\">https://doi.org/10.1093/jeb/voae052</a>.","ieee":"N. H. Barton, “Limits to species’ range: The tension between local and global adaptation,” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6. Oxford University Press, pp. 605–615, 2024.","ista":"Barton NH. 2024. Limits to species’ range: The tension between local and global adaptation. Journal of Evolutionary Biology. 37(6), 605–615.","short":"N.H. Barton, Journal of Evolutionary Biology 37 (2024) 605–615."},"article_processing_charge":"Yes (via OA deal)","status":"public","_id":"17238","page":"605-615","publication_status":"published","pmid":1,"quality_controlled":"1","publication":"Journal of Evolutionary Biology","file":[{"date_updated":"2024-07-15T09:45:25Z","relation":"main_file","success":1,"creator":"dernst","checksum":"94e6b68bddf6cadcec29c7f41647359f","content_type":"application/pdf","file_name":"2024_JourEvolutionaryBiology_Barton.pdf","access_level":"open_access","file_id":"17241","file_size":1194263,"date_created":"2024-07-15T09:45:25Z"}],"title":"Limits to species' range: The tension between local and global adaptation","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_published":"2024-06-01T00:00:00Z"},{"scopus_import":"1","acknowledgement":"We are grateful to Nancy Forde (Simon Fraser University) for her motivating comments. Financial support from the Ministerio de Ciencia, Innovación y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged. A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant No. 585 80296).","ddc":["540"],"OA_type":"hybrid","day":"16","publisher":"American Chemical Society","doi":"10.1021/acsnano.4c03839","department":[{"_id":"AnSa"}],"intvolume":"        18","year":"2024","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"}],"ec_funded":1,"OA_place":"publisher","language":[{"iso":"eng"}],"external_id":{"pmid":["38958189"],"isi":["001263155500001"]},"oa":1,"file_date_updated":"2025-01-09T12:06:48Z","date_created":"2024-07-14T22:01:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","month":"07","abstract":[{"text":"Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes.","lang":"eng"}],"volume":18,"date_updated":"2025-12-16T09:01:10Z","issue":"28","article_type":"original","_id":"17239","status":"public","article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. 2024;18(28):18485-18492. doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>","apa":"Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., &#38; Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>","ista":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 18(28), 18485–18492.","short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 18485–18492.","mla":"Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>.","chicago":"Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić, and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>.","ieee":"C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,” <i>ACS Nano</i>, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024."},"type":"journal_article","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"publication":"ACS Nano","file":[{"date_updated":"2025-01-09T12:06:48Z","checksum":"b7e9ce718e92f568bcb3810e8e28e458","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18808","file_name":"2024_ACSNano_GarciaSacristan.pdf","date_created":"2025-01-09T12:06:48Z","file_size":10036838}],"quality_controlled":"1","pmid":1,"page":"18485-18492","publication_status":"published","date_published":"2024-07-16T00:00:00Z","author":[{"first_name":"Clara","last_name":"Garcia-Sacristan","full_name":"Garcia-Sacristan, Clara"},{"first_name":"Victor G.","full_name":"Gisbert, Victor G.","last_name":"Gisbert"},{"id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398","first_name":"Kevin","last_name":"Klein","full_name":"Klein, Kevin"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Garcia","full_name":"Garcia, Ricardo","first_name":"Ricardo"}],"title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures"},{"date_published":"2024-09-01T00:00:00Z","author":[{"first_name":"Eléonore","last_name":"Vercruysse","full_name":"Vercruysse, Eléonore"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"},{"last_name":"Gómez-González","full_name":"Gómez-González, Manuel","first_name":"Manuel"},{"first_name":"Alexandre","full_name":"Remson, Alexandre","last_name":"Remson"},{"full_name":"Luciano, Marine","last_name":"Luciano","first_name":"Marine"},{"first_name":"Yohalie","full_name":"Kalukula, Yohalie","last_name":"Kalukula"},{"first_name":"Leone","last_name":"Rossetti","full_name":"Rossetti, Leone"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","publication":"Nature Physics","quality_controlled":"1","page":"1492-1500","publication_status":"published","_id":"17269","status":"public","article_processing_charge":"No","citation":{"ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. 2024;20:1492-1500. doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>","apa":"Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M., Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>","ista":"Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","short":"E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500.","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>.","chicago":"Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>.","ieee":"E. Vercruysse <i>et al.</i>, “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1492–1500, 2024."},"type":"journal_article","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"oa_version":"Preprint","isi":1,"month":"09","abstract":[{"text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.","lang":"eng"}],"volume":20,"date_updated":"2025-09-08T08:28:31Z","article_type":"original","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/","description":"News on ISTA website"}]},"OA_place":"repository","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001250246200004"]},"oa":1,"date_created":"2024-07-16T12:32:17Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.07.17.500364"}],"intvolume":"        20","year":"2024","department":[{"_id":"EdHa"}],"project":[{"grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"ec_funded":1,"OA_type":"green","day":"01","publisher":"Springer Nature","doi":"10.1038/s41567-024-02532-x","scopus_import":"1","acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business."}]