[{"article_type":"original","article_processing_charge":"No","date_updated":"2026-04-02T12:14:43Z","publication":"Nature Communications","type":"journal_article","ddc":["570"],"scopus_import":"1","file_date_updated":"2022-02-21T07:59:32Z","publication_status":"published","doi":"10.1038/s41467-022-28404-7","volume":13,"title":"Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor","year":"2022","day":"08","oa":1,"abstract":[{"text":"AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory\r\nsynapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs)\r\nleads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission\r\nand are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs)\r\nthrough currently incompletely resolved mechanisms. Here, electron cryo-microscopy\r\nstructures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states\r\n(at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’),\r\nelucidating how this TARP stabilizes specific gating states. We further show how TARPs alter\r\nchannel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we\r\nreveal that the Q/R-editing site couples the channel constriction at the filter entrance to the\r\ngate, and forms the major cation binding site in the conduction path. Our results provide a\r\nmechanistic framework of how TARPs modulate AMPAR gating and conductance.","lang":"eng"}],"language":[{"iso":"eng"}],"article_number":"734","citation":{"short":"B. Herguedas, B.K. Kohegyi, J.N. Dohrke, J. Watson, D. Zhang, H. Ho, S.A. Shaikh, R. Lape, J.M. Krieger, I.H. Greger, Nature Communications 13 (2022).","mla":"Herguedas, Beatriz, et al. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” <i>Nature Communications</i>, vol. 13, 734, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-28404-7\">10.1038/s41467-022-28404-7</a>.","ista":"Herguedas B, Kohegyi BK, Dohrke JN, Watson J, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. 2022. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nature Communications. 13, 734.","chicago":"Herguedas, Beatriz, Bianka K. Kohegyi, Jan Niklas Dohrke, Jake Watson, Danyang Zhang, Hinze Ho, Saher A. Shaikh, Remigijus Lape, James M. Krieger, and Ingo H. Greger. “Mechanisms Underlying TARP Modulation of the GluA1/2-Γ8 AMPA Receptor.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-28404-7\">https://doi.org/10.1038/s41467-022-28404-7</a>.","ieee":"B. Herguedas <i>et al.</i>, “Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","apa":"Herguedas, B., Kohegyi, B. K., Dohrke, J. N., Watson, J., Zhang, D., Ho, H., … Greger, I. H. (2022). Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-28404-7\">https://doi.org/10.1038/s41467-022-28404-7</a>","ama":"Herguedas B, Kohegyi BK, Dohrke JN, et al. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-28404-7\">10.1038/s41467-022-28404-7</a>"},"publisher":"Springer Nature","department":[{"_id":"PeJo"}],"date_created":"2022-02-20T23:01:30Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","month":"02","date_published":"2022-02-08T00:00:00Z","quality_controlled":"1","intvolume":"        13","publication_identifier":{"eissn":["2041-1723"]},"_id":"10763","author":[{"full_name":"Herguedas, Beatriz","last_name":"Herguedas","first_name":"Beatriz"},{"full_name":"Kohegyi, Bianka K.","first_name":"Bianka K.","last_name":"Kohegyi"},{"full_name":"Dohrke, Jan Niklas","last_name":"Dohrke","first_name":"Jan Niklas"},{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake"},{"full_name":"Zhang, Danyang","last_name":"Zhang","first_name":"Danyang"},{"last_name":"Ho","first_name":"Hinze","full_name":"Ho, Hinze"},{"full_name":"Shaikh, Saher A.","first_name":"Saher A.","last_name":"Shaikh"},{"last_name":"Lape","first_name":"Remigijus","full_name":"Lape, Remigijus"},{"full_name":"Krieger, James M.","last_name":"Krieger","first_name":"James M."},{"last_name":"Greger","first_name":"Ingo H.","full_name":"Greger, Ingo H."}],"pmid":1,"external_id":{"isi":["000757297200008"],"pmid":["35136046"]},"isi":1,"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","acknowledgement":"We thank Ondrej Cais for critical reading of the manuscript. We are grateful to LMB\r\nscientific computing and the EM facility for support, Paul Emsley for help with model\r\nbuilding and Takanori Nakane for helpful comments with Relion 3.1. This work was\r\nsupported by grants from the Medical Research Council (MC_U105174197) and BBSRC\r\n(BB/N002113/1) to I.H.G, and grants from the MCIN/AEI/ 10.13039/501100011033 and\r\n“ESF Investing in your future” to B.H (PID2019-106284GA-I00 and RYC2018-025720-I).","file":[{"file_name":"2022_NatureCommunications_Herguedas.pdf","checksum":"d86ee8eabe8b794730729ffbb1a8832e","success":1,"file_size":2625540,"access_level":"open_access","relation":"main_file","date_created":"2022-02-21T07:59:32Z","content_type":"application/pdf","creator":"dernst","file_id":"10778","date_updated":"2022-02-21T07:59:32Z"}]},{"OA_place":"publisher","author":[{"last_name":"Daguerre","first_name":"L.","full_name":"Daguerre, L."},{"last_name":"Torroba","first_name":"G.","full_name":"Torroba, G."},{"last_name":"Medina Ramos","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A"},{"first_name":"M.","last_name":"Solís","full_name":"Solís, M."}],"DOAJ_listed":"1","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledgement":"Se agradece a Horacio Casini por distintas discusiones y comentarios a lo largo del trabajo. LD cuenta con el apoyo de CNEA y UNCuyo, Inst. GT cuenta con el apoyo de CONICET,\r\nANPCyT, CNEA, y UNCuyo, Inst. Balseiro. RM cuenta con el apoyo de IST Austria. MS cuenta con el apoyode CONICET y UNCuyo, Inst. Balseiro. También se agradece a la Asociación Argentina de Física por la posibilidad de presentar este artículo en el marco de una Mención Especial por el Premio Luis Másperi 2020.","has_accepted_license":"1","file":[{"date_created":"2022-02-21T09:32:44Z","relation":"main_file","access_level":"open_access","checksum":"ca66a3017205677c5b4d22b3bb74fb0b","success":1,"file_size":4505751,"file_name":"2022_AnalesAFA_Daguerre.pdf","date_updated":"2022-02-21T09:32:44Z","file_id":"10782","creator":"dernst","content_type":"application/pdf"}],"date_created":"2022-02-20T23:01:32Z","department":[{"_id":"MaSe"}],"citation":{"ista":"Daguerre L, Torroba G, Medina Ramos RA, Solís M. 2022. Non relativistic quantum field theory: Dynamics and irreversibility. Anales de la Asociacion Fisica Argentina. 32(4), 93–98.","mla":"Daguerre, L., et al. “Non relativistic quantum field theory: Dynamics and irreversibility.” <i>Anales de la Asociacion Fisica Argentina</i>, vol. 32, no. 4, Asociación Física Argentina, 2022, pp. 93–98, doi:<a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">10.31527/analesafa.2021.32.4.93</a>.","short":"L. Daguerre, G. Torroba, R.A. Medina Ramos, M. Solís, Anales de la Asociacion Fisica Argentina 32 (2022) 93–98.","chicago":"Daguerre, L., G. Torroba, Raimel A Medina Ramos, and M. Solís. “Non relativistic quantum field theory: Dynamics and irreversibility.” <i>Anales de la Asociacion Fisica Argentina</i>. Asociación Física Argentina, 2022. <a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">https://doi.org/10.31527/analesafa.2021.32.4.93</a>.","apa":"Daguerre, L., Torroba, G., Medina Ramos, R. A., &#38; Solís, M. (2022). Non relativistic quantum field theory: Dynamics and irreversibility. <i>Anales de la Asociacion Fisica Argentina</i>. Asociación Física Argentina. <a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">https://doi.org/10.31527/analesafa.2021.32.4.93</a>","ama":"Daguerre L, Torroba G, Medina Ramos RA, Solís M. Non relativistic quantum field theory: Dynamics and irreversibility. <i>Anales de la Asociacion Fisica Argentina</i>. 2022;32(4):93-98. doi:<a href=\"https://doi.org/10.31527/analesafa.2021.32.4.93\">10.31527/analesafa.2021.32.4.93</a>","ieee":"L. Daguerre, G. Torroba, R. A. Medina Ramos, and M. Solís, “Non relativistic quantum field theory: Dynamics and irreversibility,” <i>Anales de la Asociacion Fisica Argentina</i>, vol. 32, no. 4. Asociación Física Argentina, pp. 93–98, 2022."},"publisher":"Asociación Física Argentina","status":"public","month":"01","page":"93-98","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","date_published":"2022-01-13T00:00:00Z","issue":"4","publication_identifier":{"eissn":["1850-1168"]},"intvolume":"        32","_id":"10769","file_date_updated":"2022-02-21T09:32:44Z","doi":"10.31527/analesafa.2021.32.4.93","publication_status":"published","day":"13","OA_type":"gold","oa":1,"title":"Non relativistic quantum field theory: Dynamics and irreversibility","volume":32,"year":"2022","language":[{"iso":"spa"}],"abstract":[{"lang":"eng","text":"studiamos aspectos de Teoría Cuántica de Campos a densidad finita usando técnicas y conceptos de información cuántica. Nos enfocamos en fermiones de Dirac masivos con potencial químico en 1+1 dimensiones espacio-temporales. Usando la entropía de entrelazamiento en un intervalo, construimos la función c entrópica que es finita. Esta función c no es monótona, e incorpora el entrelazamiento de largo alcance proveniente de la superficie de Fermi. Motivados por trabajos previos de modelos en la red, calculamos numéricamente las entropías de Renyi y encontramos oscilaciones de Friedel. Seguidamente, analizamos la información mutua como una medida de correlación entre diferentes regiones. Usando una expansión de distancia grande desarrollada por Cardy, argumentamos que la información mutua detecta las correlaciones inducidas por la superficie de Fermi todavía al orden dominante en la expansión. Finalmente, analizamos la entropía relativa y sus generalizaciones de Renyi para distinguir estados con diferente carga. Encontramos que estados en diferentes sectores de superselección dan origen a un comportamiento super-extensivo en la entropía relativa."}],"article_processing_charge":"No","article_type":"original","date_updated":"2026-04-02T12:30:12Z","type":"journal_article","publication":"Anales de la Asociacion Fisica Argentina","ddc":["530"],"scopus_import":"1"},{"month":"05","status":"public","department":[{"_id":"RySh"}],"date_created":"2022-04-24T22:01:44Z","publisher":"Wiley","citation":{"ieee":"S. Thayyil <i>et al.</i>, “Dynamic control of microbial movement by photoswitchable ATP antagonists,” <i>Chemistry - A European Journal</i>, vol. 28, no. 30. Wiley, 2022.","apa":"Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa, K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable ATP antagonists. <i>Chemistry - A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.202200807\">https://doi.org/10.1002/chem.202200807</a>","ama":"Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement by photoswitchable ATP antagonists. <i>Chemistry - A European Journal</i>. 2022;28(30). doi:<a href=\"https://doi.org/10.1002/chem.202200807\">10.1002/chem.202200807</a>","ista":"Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M, Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.","short":"S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J. Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).","mla":"Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” <i>Chemistry - A European Journal</i>, vol. 28, no. 30, e202200807, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/chem.202200807\">10.1002/chem.202200807</a>.","chicago":"Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim, Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.” <i>Chemistry - A European Journal</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/chem.202200807\">https://doi.org/10.1002/chem.202200807</a>."},"_id":"11333","issue":"30","publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"intvolume":"        28","quality_controlled":"1","date_published":"2022-05-25T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","isi":1,"external_id":{"pmid":["35332959"],"isi":["000781658800001"]},"author":[{"full_name":"Thayyil, Sampreeth","first_name":"Sampreeth","last_name":"Thayyil"},{"full_name":"Nishigami, Yukinori","first_name":"Yukinori","last_name":"Nishigami"},{"last_name":"Islam","first_name":"Muhammad J","full_name":"Islam, Muhammad J","id":"C94881D2-008F-11EA-8E08-2637E6697425"},{"full_name":"Hashim, P. K.","last_name":"Hashim","first_name":"P. K."},{"first_name":"Ken'Ya","last_name":"Furuta","full_name":"Furuta, Ken'Ya"},{"full_name":"Oiwa, Kazuhiro","last_name":"Oiwa","first_name":"Kazuhiro"},{"last_name":"Yu","first_name":"Jian","full_name":"Yu, Jian"},{"first_name":"Min","last_name":"Yao","full_name":"Yao, Min"},{"first_name":"Toshiyuki","last_name":"Nakagaki","full_name":"Nakagaki, Toshiyuki"},{"last_name":"Tamaoki","first_name":"Nobuyuki","full_name":"Tamaoki, Nobuyuki"}],"pmid":1,"article_processing_charge":"No","article_type":"original","scopus_import":"1","publication":"Chemistry - A European Journal","type":"journal_article","date_updated":"2026-04-02T11:59:00Z","doi":"10.1002/chem.202200807","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1002/chem.202200807","open_access":"1"}],"language":[{"iso":"eng"}],"article_number":"e202200807","abstract":[{"text":"Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site.","lang":"eng"}],"oa":1,"day":"25","year":"2022","volume":28,"title":"Dynamic control of microbial movement by photoswitchable ATP antagonists"},{"doi":"10.1073/pnas.2122030119","publication_status":"published","file_date_updated":"2022-02-21T08:45:11Z","ec_funded":1,"language":[{"iso":"eng"}],"article_number":"e2122030119","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact."}],"corr_author":"1","day":"14","oa":1,"volume":119,"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","year":"2022","article_processing_charge":"No","article_type":"original","ddc":["570"],"scopus_import":"1","date_updated":"2026-04-02T12:54:56Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9750"}]},"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"pmid":1,"author":[{"last_name":"Slovakova","first_name":"Jana","full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"},{"last_name":"Arslan","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N"},{"id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346","last_name":"Caballero Mancebo","first_name":"Silvia"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel"},{"last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"external_id":{"pmid":["35165179"],"isi":["000766926900009"]},"has_accepted_license":"1","acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda  for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","file":[{"file_id":"10780","date_updated":"2022-02-21T08:45:11Z","creator":"dernst","content_type":"application/pdf","date_created":"2022-02-21T08:45:11Z","access_level":"open_access","relation":"main_file","file_name":"2022_PNAS_Slovakova.pdf","checksum":"d49f83c3580613966f71768ddb9a55a5","success":1,"file_size":1609678}],"status":"public","month":"02","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_created":"2022-02-20T23:01:31Z","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"citation":{"short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8, e2122030119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>.","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122030119\">https://doi.org/10.1073/pnas.2122030119</a>","ieee":"J. Slovakova <i>et al.</i>, “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 8. National Academy of Sciences, 2022.","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(8). doi:<a href=\"https://doi.org/10.1073/pnas.2122030119\">10.1073/pnas.2122030119</a>"},"publisher":"National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"]},"issue":"8","intvolume":"       119","_id":"10766","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"_id":"2521E28E-B435-11E9-9278-68D0E5697425","name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013"}],"quality_controlled":"1","date_published":"2022-02-14T00:00:00Z"},{"publication_identifier":{"eissn":["2691-3399"]},"issue":"2","intvolume":"         3","_id":"11353","quality_controlled":"1","project":[{"_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","grant_number":"732894"}],"date_published":"2022-04-13T00:00:00Z","status":"public","month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"JoFi"}],"date_created":"2022-05-08T22:01:43Z","citation":{"apa":"Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., &#38; Kippenberg, T. J. (2022). Dissipative quantum feedback in measurements using a parametrically coupled microcavity. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">https://doi.org/10.1103/PRXQuantum.3.020309</a>","ieee":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative quantum feedback in measurements using a parametrically coupled microcavity,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","ama":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">10.1103/PRXQuantum.3.020309</a>","chicago":"Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">https://doi.org/10.1103/PRXQuantum.3.020309</a>.","ista":"Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative quantum feedback in measurements using a parametrically coupled microcavity. PRX Quantum. 3(2), 020309.","mla":"Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically Coupled Microcavity.” <i>PRX Quantum</i>, vol. 3, no. 2, 020309, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.3.020309\">10.1103/PRXQuantum.3.020309</a>.","short":"L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum 3 (2022)."},"publisher":"American Physical Society","acknowledgement":"L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel, P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further supported by Swiss National Science Foundation under Grant Agreements No. 185870 (Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology (CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich.","has_accepted_license":"1","file":[{"file_id":"11358","date_updated":"2022-05-09T07:10:51Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2022-05-09T07:10:51Z","checksum":"35ff9ddf1d54f64432e435b660edaeb6","file_size":1657177,"success":1,"file_name":"2022_PRXQuantum_Qiu.pdf"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"author":[{"orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","first_name":"Liu"},{"full_name":"Huang, Guanhao","last_name":"Huang","first_name":"Guanhao"},{"last_name":"Shomroni","first_name":"Itay","full_name":"Shomroni, Itay"},{"full_name":"Pan, Jiahe","last_name":"Pan","first_name":"Jiahe"},{"first_name":"Paul","last_name":"Seidler","full_name":"Seidler, Paul"},{"last_name":"Kippenberg","first_name":"Tobias J.","full_name":"Kippenberg, Tobias J."}],"external_id":{"isi":["000789316700001"]},"ddc":["530"],"scopus_import":"1","date_updated":"2026-04-02T12:30:47Z","publication":"PRX Quantum","type":"journal_article","article_processing_charge":"No","article_type":"original","article_number":"020309","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Micro- and nanoscale optical or microwave cavities are used in a wide range of classical applications and quantum science experiments, ranging from precision measurements, laser technologies to quantum control of mechanical motion. The dissipative photon loss via absorption, present to some extent in any optical cavity, is known to introduce thermo-optical effects and thereby impose fundamental limits on precision measurements. Here, we theoretically and experimentally reveal that such dissipative photon absorption can result in quantum feedback via in-loop field detection of the absorbed optical field, leading to the intracavity field fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum feedback to the cavity field arises. Strikingly, this modifies the optical cavity susceptibility in coherent response measurements (capable of both increasing or decreasing the bare cavity linewidth) and causes excess noise and correlations in incoherent interferometric optomechanical measurements using a cavity, that is parametrically coupled to a mechanical oscillator. We experimentally observe such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled optomechanical crystal cavitiess at both cryogenic temperature (approximately 8 K) and ambient conditions. The dissipative feedback introduces effective modifications to the optical cavity linewidth and the optomechanical scattering rate and gives rise to excess imprecision noise in the interferometric quantum measurement of mechanical motion. Such dissipative feedback differs fundamentally from a quantum nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback itself always results in an antisqueezed out-of-loop optical field, while it can enhance the coexisting Kerr squeezing under certain conditions. Our result applies to cavity spectroscopy in both optical and superconducting microwave cavities, and equally applies to any dissipative feedback mechanism of different bandwidth inside the cavity. It has wide-ranging implications for future dissipation engineering, such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency conversion, and nonreciprocity in photonic systems."}],"day":"13","oa":1,"title":"Dissipative quantum feedback in measurements using a parametrically coupled microcavity","volume":3,"year":"2022","doi":"10.1103/PRXQuantum.3.020309","publication_status":"published","file_date_updated":"2022-05-09T07:10:51Z","ec_funded":1},{"doi":"10.7554/eLife.68040","publication_status":"published","file_date_updated":"2022-03-07T07:39:25Z","language":[{"iso":"eng"}],"article_number":"e68040","abstract":[{"lang":"eng","text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome."}],"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa":1,"day":"24","year":"2022","volume":11,"title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","article_processing_charge":"No","article_type":"original","scopus_import":"1","ddc":["570"],"type":"journal_article","publication":"eLife","date_updated":"2026-04-02T12:45:39Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","isi":1,"external_id":{"isi":["000763432300001"],"pmid":["35201977"]},"author":[{"first_name":"Giulio","last_name":"Valperga","orcid":"0000-0001-6726-3890","full_name":"Valperga, Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E"},{"full_name":"De Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"De Bono"}],"pmid":1,"file":[{"checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","file_size":4095591,"success":1,"file_name":"2022_eLife_Valperga.pdf","relation":"main_file","access_level":"open_access","date_created":"2022-03-07T07:39:25Z","content_type":"application/pdf","creator":"dernst","date_updated":"2022-03-07T07:39:25Z","file_id":"10830"}],"has_accepted_license":"1","acknowledgement":"We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB).","month":"02","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_created":"2022-03-06T23:01:52Z","department":[{"_id":"MaDe"}],"citation":{"ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>","apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>.","short":"G. Valperga, M. de Bono, ELife 11 (2022).","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040."},"publisher":"eLife Sciences Publications","_id":"10826","intvolume":"        11","publication_identifier":{"eissn":["2050-084X"]},"project":[{"grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function"}],"quality_controlled":"1","date_published":"2022-02-24T00:00:00Z"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"status":"public","id":"10833","relation":"research_data"}]},"oa_version":"Published Version","isi":1,"external_id":{"isi":["000765113000016"],"pmid":["35134289"]},"author":[{"last_name":"Hasler","first_name":"Roger","full_name":"Hasler, Roger"},{"full_name":"Reiner-Rozman, Ciril","first_name":"Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","first_name":"Stefan","last_name":"Fossati"},{"first_name":"Patrik","last_name":"Aspermair","full_name":"Aspermair, Patrik"},{"first_name":"Jakub","last_name":"Dostalek","full_name":"Dostalek, Jakub"},{"orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho","first_name":"Seungho","last_name":"Lee"},{"last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Bintinger, Johannes","last_name":"Bintinger","first_name":"Johannes"},{"last_name":"Knoll","first_name":"Wolfgang","full_name":"Knoll, Wolfgang"}],"pmid":1,"file":[{"date_created":"2022-03-07T08:15:01Z","access_level":"open_access","relation":"main_file","file_name":"2022_ACSSensors_Hasler.pdf","checksum":"d704af7262cd484da9bb84b7d84e2b09","file_size":2969415,"success":1,"file_id":"10832","date_updated":"2022-03-07T08:15:01Z","creator":"dernst","content_type":"application/pdf"}],"has_accepted_license":"1","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research. The data that support the findings of this study are openly available in Zenodo (DOI: 10.5281/zenodo.5500360)","month":"02","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"page":"504-512","date_created":"2022-03-06T23:01:54Z","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","citation":{"chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>.","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. 7(2), 504–512.","mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, ACS Sensors 7 (2022) 504–512.","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” <i>ACS Sensors</i>, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. 2022;7(2):504-512. doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>"},"_id":"10829","intvolume":"         7","issue":"2","publication_identifier":{"eissn":["2379-3694"]},"quality_controlled":"1","date_published":"2022-02-08T00:00:00Z","doi":"10.1021/acssensors.1c02313","publication_status":"published","file_date_updated":"2022-03-07T08:15:01Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"A novel multivariable system, combining a transistor with fiber optic-based surface plasmon resonance spectroscopy with the gate electrode simultaneously acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows for discrimination of mass and charge contributions for binding assays on the same sensor surface. Furthermore, we optimize the sensor geometry by investigating the influence of the fiber area to transistor channel area ratio and distance. We show that larger fiber optic tip diameters are favorable for electronic and optical signals and demonstrate the reversibility of plasmon resonance wavelength shifts after electric field application. As a proof of principle, a layer-by-layer assembly of polyelectrolytes is performed to benchmark the system against multivariable sensing platforms with planar surface plasmon resonance configurations. Furthermore, the biosensing performance is assessed using a thrombin binding assay with surface-immobilized aptamers as receptors, allowing for the detection of medically relevant thrombin concentrations."}],"oa":1,"day":"08","year":"2022","volume":7,"title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","article_processing_charge":"No","article_type":"original","scopus_import":"1","ddc":["540"],"type":"journal_article","publication":"ACS Sensors","date_updated":"2026-04-02T12:33:46Z"},{"volume":156,"title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","year":"2022","day":"16","oa":1,"abstract":[{"text":"Titanium dioxide has been extensively studied in the rutile or anatase phase, while its high-pressure phases are less well-understood, despite that many are thought to have interesting optical, mechanical, and electrochemical properties. First-principles methods, such as density functional theory (DFT), are often used to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus, impractical for long time scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stabilities of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO2, we design an empirical model as a baseline and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called Δ-learning potential contains long-range electrostatic interactions and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range 0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition processes by compressing anatase at different temperatures. At 300 K, we predominantly observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic two-step mechanism with a highly ordered and collective atomic motion. At 2000 K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases, and our method is generally applicable to other functional materials with multiple polymorphs.","lang":"eng"}],"corr_author":"1","article_number":"074106","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.12968"}],"publication_status":"published","doi":"10.1063/5.0079844","date_updated":"2026-04-02T12:37:16Z","type":"journal_article","publication":"The Journal of chemical physics","scopus_import":"1","article_type":"original","article_processing_charge":"No","acknowledgement":"J.G.L. and B.C. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).","author":[{"first_name":"Jacob G.","last_name":"Lee","full_name":"Lee, Jacob G."},{"full_name":"Pickard, Chris J.","last_name":"Pickard","first_name":"Chris J."},{"last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"pmid":1,"arxiv":1,"external_id":{"isi":["000796704500014"],"pmid":["35183078"],"arxiv":["2111.12968"]},"isi":1,"oa_version":"Preprint","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2022-02-16T00:00:00Z","quality_controlled":"1","publication_identifier":{"eissn":["1089-7690"]},"intvolume":"       156","issue":"7","_id":"10827","citation":{"chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>.","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>.","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” <i>The Journal of chemical physics</i>, vol. 156, no. 7. AIP Publishing, 2022.","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of chemical physics</i>. 2022;156(7). doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>","apa":"Lee, J. G., Pickard, C. J., &#38; Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>"},"publisher":"AIP Publishing","date_created":"2022-03-06T23:01:53Z","department":[{"_id":"BiCh"}],"status":"public","month":"02"},{"isi":1,"pmid":1,"author":[{"full_name":"Evers, Ferdinand","last_name":"Evers","first_name":"Ferdinand"},{"first_name":"Amnon","last_name":"Aharony","full_name":"Aharony, Amnon"},{"full_name":"Bar-Gill, Nir","last_name":"Bar-Gill","first_name":"Nir"},{"first_name":"Ora","last_name":"Entin-Wohlman","full_name":"Entin-Wohlman, Ora"},{"full_name":"Hedegård, Per","last_name":"Hedegård","first_name":"Per"},{"full_name":"Hod, Oded","first_name":"Oded","last_name":"Hod"},{"full_name":"Jelinek, Pavel","first_name":"Pavel","last_name":"Jelinek"},{"full_name":"Kamieniarz, Grzegorz","last_name":"Kamieniarz","first_name":"Grzegorz"},{"first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Karen","last_name":"Michaeli","full_name":"Michaeli, Karen"},{"last_name":"Mujica","first_name":"Vladimiro","full_name":"Mujica, Vladimiro"},{"first_name":"Ron","last_name":"Naaman","full_name":"Naaman, Ron"},{"full_name":"Paltiel, Yossi","last_name":"Paltiel","first_name":"Yossi"},{"last_name":"Refaely-Abramson","first_name":"Sivan","full_name":"Refaely-Abramson, Sivan"},{"full_name":"Tal, Oren","last_name":"Tal","first_name":"Oren"},{"last_name":"Thijssen","first_name":"Jos","full_name":"Thijssen, Jos"},{"last_name":"Thoss","first_name":"Michael","full_name":"Thoss, Michael"},{"last_name":"Van Ruitenbeek","first_name":"Jan M.","full_name":"Van Ruitenbeek, Jan M."},{"full_name":"Venkataraman, Latha","last_name":"Venkataraman","first_name":"Latha"},{"full_name":"Waldeck, David H.","last_name":"Waldeck","first_name":"David H."},{"first_name":"Binghai","last_name":"Yan","full_name":"Yan, Binghai"},{"full_name":"Kronik, Leeor","first_name":"Leeor","last_name":"Kronik"}],"arxiv":1,"external_id":{"isi":["000753795900001"],"pmid":["35064943"],"arxiv":["2108.09998"]},"oa_version":"Preprint","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","date_published":"2022-04-01T00:00:00Z","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"intvolume":"        34","issue":"13","_id":"10771","department":[{"_id":"MiLe"}],"date_created":"2022-02-20T23:01:33Z","publisher":"Wiley","citation":{"apa":"Evers, F., Aharony, A., Bar-Gill, N., Entin-Wohlman, O., Hedegård, P., Hod, O., … Kronik, L. (2022). Theory of chirality induced spin selectivity: Progress and challenges. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202106629\">https://doi.org/10.1002/adma.202106629</a>","ama":"Evers F, Aharony A, Bar-Gill N, et al. Theory of chirality induced spin selectivity: Progress and challenges. <i>Advanced Materials</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1002/adma.202106629\">10.1002/adma.202106629</a>","ieee":"F. Evers <i>et al.</i>, “Theory of chirality induced spin selectivity: Progress and challenges,” <i>Advanced Materials</i>, vol. 34, no. 13. Wiley, 2022.","chicago":"Evers, Ferdinand, Amnon Aharony, Nir Bar-Gill, Ora Entin-Wohlman, Per Hedegård, Oded Hod, Pavel Jelinek, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” <i>Advanced Materials</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/adma.202106629\">https://doi.org/10.1002/adma.202106629</a>.","ista":"Evers F, Aharony A, Bar-Gill N, Entin-Wohlman O, Hedegård P, Hod O, Jelinek P, Kamieniarz G, Lemeshko M, Michaeli K, Mujica V, Naaman R, Paltiel Y, Refaely-Abramson S, Tal O, Thijssen J, Thoss M, Van Ruitenbeek JM, Venkataraman L, Waldeck DH, Yan B, Kronik L. 2022. Theory of chirality induced spin selectivity: Progress and challenges. Advanced Materials. 34(13), 2106629.","short":"F. Evers, A. Aharony, N. Bar-Gill, O. Entin-Wohlman, P. Hedegård, O. Hod, P. Jelinek, G. Kamieniarz, M. Lemeshko, K. Michaeli, V. Mujica, R. Naaman, Y. Paltiel, S. Refaely-Abramson, O. Tal, J. Thijssen, M. Thoss, J.M. Van Ruitenbeek, L. Venkataraman, D.H. Waldeck, B. Yan, L. Kronik, Advanced Materials 34 (2022).","mla":"Evers, Ferdinand, et al. “Theory of Chirality Induced Spin Selectivity: Progress and Challenges.” <i>Advanced Materials</i>, vol. 34, no. 13, 2106629, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/adma.202106629\">10.1002/adma.202106629</a>."},"status":"public","month":"04","day":"01","oa":1,"title":"Theory of chirality induced spin selectivity: Progress and challenges","volume":34,"year":"2022","article_number":"2106629","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"A critical overview of the theory of the chirality-induced spin selectivity (CISS) effect, that is, phenomena in which the chirality of molecular species imparts significant spin selectivity to various electron processes, is provided. Based on discussions in a recently held workshop, and further work published since, the status of CISS effects—in electron transmission, electron transport, and chemical reactions—is reviewed. For each, a detailed discussion of the state-of-the-art in theoretical understanding is provided and remaining challenges and research opportunities are identified."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.09998"}],"doi":"10.1002/adma.202106629","publication_status":"published","date_updated":"2026-04-02T12:45:15Z","publication":"Advanced Materials","type":"journal_article","scopus_import":"1","article_processing_charge":"No","article_type":"review"},{"ddc":["540"],"_id":"10833","date_published":"2022-02-08T00:00:00Z","date_updated":"2026-04-02T12:33:44Z","type":"research_data_reference","status":"public","article_processing_charge":"No","month":"02","publisher":"Zenodo","citation":{"chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>.","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","mla":"Hasler, Roger, et al. <i>Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022.","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>"},"department":[{"_id":"MaIb"}],"date_created":"2022-03-07T08:19:11Z","abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","year":"2022","day":"08","oa":1,"related_material":{"record":[{"id":"10829","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5281/ZENODO.5500360","author":[{"last_name":"Hasler","first_name":"Roger","full_name":"Hasler, Roger"},{"full_name":"Reiner-Rozman, Ciril","first_name":"Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","first_name":"Stefan","last_name":"Fossati"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"first_name":"Seungho","last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"full_name":"Bintinger, Johannes","first_name":"Johannes","last_name":"Bintinger"},{"full_name":"Knoll, Wolfgang","first_name":"Wolfgang","last_name":"Knoll"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.5500360"}]},{"external_id":{"pmid":[" 35739187"],"isi":["000815098500002"]},"author":[{"first_name":"David","last_name":"Molina-Granada","full_name":"Molina-Granada, David"},{"first_name":"Emiliano","last_name":"González-Vioque","full_name":"González-Vioque, Emiliano"},{"last_name":"Dibley","first_name":"Marris G.","full_name":"Dibley, Marris G."},{"first_name":"Raquel","last_name":"Cabrera-Pérez","full_name":"Cabrera-Pérez, Raquel"},{"full_name":"Vallbona-Garcia, Antoni","last_name":"Vallbona-Garcia","first_name":"Antoni"},{"last_name":"Torres-Torronteras","first_name":"Javier","full_name":"Torres-Torronteras, Javier"},{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"},{"first_name":"Michael T.","last_name":"Ryan","full_name":"Ryan, Michael T."},{"last_name":"Cámara","first_name":"Yolanda","full_name":"Cámara, Yolanda"},{"first_name":"Ramon","last_name":"Martí","full_name":"Martí, Ramon"}],"pmid":1,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","file":[{"file_name":"2022_communicationsbiology_Molina-Granada.pdf","file_size":2335369,"checksum":"965f88bbcef3fd0c3e121340555c4467","success":1,"access_level":"open_access","relation":"main_file","date_created":"2022-07-13T07:44:58Z","content_type":"application/pdf","creator":"kschuh","date_updated":"2022-07-13T07:44:58Z","file_id":"11571"}],"has_accepted_license":"1","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","citation":{"mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620.","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>","ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022."},"publisher":"Springer Nature","date_created":"2022-07-10T22:01:52Z","department":[{"_id":"LeSa"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"06","status":"public","date_published":"2022-06-23T00:00:00Z","quality_controlled":"1","_id":"11551","intvolume":"         5","publication_identifier":{"eissn":["2399-3642"]},"issue":"1","file_date_updated":"2022-07-13T07:44:58Z","publication_status":"published","doi":"10.1038/s42003-022-03568-6","year":"2022","title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","volume":5,"oa":1,"day":"23","abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"article_number":"620","language":[{"iso":"eng"}],"article_processing_charge":"No","type":"journal_article","publication":"Communications Biology","date_updated":"2026-04-02T13:22:53Z","scopus_import":"1","ddc":["570"]},{"_id":"12101","publication_identifier":{"isbn":["9783959772617"],"issn":["1868-8969"]},"intvolume":"       250","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"quality_controlled":"1","date_published":"2022-12-14T00:00:00Z","month":"12","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"KrCh"}],"date_created":"2023-01-01T23:00:50Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Complexity of Spatial Games.” In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11</a>.","mla":"Chatterjee, Krishnendu, et al. “Complexity of Spatial Games.” <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 250, 11:1-11:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">10.4230/LIPIcs.FSTTCS.2022.11</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2022. Complexity of spatial games. 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science vol. 250, 11:1-11:14.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Complexity of spatial games. In: <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">10.4230/LIPIcs.FSTTCS.2022.11</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., &#38; Svoboda, J. (2022). Complexity of spatial games. In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 250). Madras, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.11</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Complexity of spatial games,” in <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Madras, India, 2022, vol. 250."},"file":[{"relation":"main_file","access_level":"open_access","date_created":"2023-01-20T10:19:19Z","checksum":"a21e3ba2421e2c4a06aa2cb6d530ede1","success":1,"file_size":657396,"file_name":"2022_LIPICs_Chatterjee.pdf","file_id":"12323","date_updated":"2023-01-20T10:19:19Z","content_type":"application/pdf","creator":"dernst"}],"acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the ERC CoG 863818\r\n(ForM-SMArt).\r\nIsmaël Jecker: The research was partially supported by the ERC grant 950398 (INFSYS).\r\nJakub Svoboda: The research was partially supported by the ERC CoG 863818 (ForM-SMArt)","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"20138","relation":"dissertation_contains"}]},"oa_version":"Published Version","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"last_name":"Jecker","first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R"},{"orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","last_name":"Svoboda","first_name":"Jakub"}],"scopus_import":"1","ddc":["000"],"publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","type":"conference","date_updated":"2026-04-07T11:49:11Z","article_processing_charge":"No","article_number":"11:1-11:14","language":[{"iso":"eng"}],"abstract":[{"text":"Spatial games form a widely-studied class of games from biology and physics modeling the evolution of social behavior. Formally, such a game is defined by a square (d by d) payoff matrix M and an undirected graph G. Each vertex of G represents an individual, that initially follows some strategy i ∈ {1,2,…,d}. In each round of the game, every individual plays the matrix game with each of its neighbors: An individual following strategy i meeting a neighbor following strategy j receives a payoff equal to the entry (i,j) of M. Then, each individual updates its strategy to its neighbors' strategy with the highest sum of payoffs, and the next round starts. The basic computational problems consist of reachability between configurations and the average frequency of a strategy. For general spatial games and graphs, these problems are in PSPACE. In this paper, we examine restricted setting: the game is a prisoner’s dilemma; and G is a subgraph of grid. We prove that basic computational problems for spatial games with prisoner’s dilemma on a subgraph of a grid are PSPACE-hard.","lang":"eng"}],"corr_author":"1","oa":1,"conference":{"start_date":"2022-12-18","end_date":"2022-12-20","location":"Madras, India","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"day":"14","year":"2022","volume":250,"title":"Complexity of spatial games","doi":"10.4230/LIPIcs.FSTTCS.2022.11","publication_status":"published","file_date_updated":"2023-01-20T10:19:19Z","ec_funded":1},{"acknowledgement":"K.C. acknowledges support from ERC Start Grant No. (279307: Graph Games), ERC Consolidator Grant No. (863818: ForM-SMart), and Austrian Science Fund (FWF)\r\nGrants No. P23499-N23 and No. S11407-N23 (RiSE). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385.","isi":1,"external_id":{"isi":["000870243100001"],"arxiv":["2210.02394"]},"arxiv":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Svoboda","first_name":"Jakub","orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20138"}]},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"quality_controlled":"1","date_published":"2022-09-29T00:00:00Z","_id":"12257","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"intvolume":"       106","issue":"3","department":[{"_id":"KrCh"}],"date_created":"2023-01-16T09:57:57Z","citation":{"chicago":"Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis, and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” <i>Physical Review E</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physreve.106.034321\">https://doi.org/10.1103/physreve.106.034321</a>.","mla":"Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” <i>Physical Review E</i>, vol. 106, no. 3, 034321, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physreve.106.034321\">10.1103/physreve.106.034321</a>.","short":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical Review E 106 (2022).","ista":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. 2022. Social balance on networks: Local minima and best-edge dynamics. Physical Review E. 106(3), 034321.","ama":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance on networks: Local minima and best-edge dynamics. <i>Physical Review E</i>. 2022;106(3). doi:<a href=\"https://doi.org/10.1103/physreve.106.034321\">10.1103/physreve.106.034321</a>","apa":"Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., &#38; Tkadlec, J. (2022). Social balance on networks: Local minima and best-edge dynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.106.034321\">https://doi.org/10.1103/physreve.106.034321</a>","ieee":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social balance on networks: Local minima and best-edge dynamics,” <i>Physical Review E</i>, vol. 106, no. 3. American Physical Society, 2022."},"publisher":"American Physical Society","month":"09","status":"public","oa":1,"day":"29","year":"2022","title":"Social balance on networks: Local minima and best-edge dynamics","volume":106,"article_number":"034321","language":[{"iso":"eng"}],"abstract":[{"text":"Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.02394","open_access":"1"}],"ec_funded":1,"doi":"10.1103/physreve.106.034321","publication_status":"published","type":"journal_article","publication":"Physical Review E","date_updated":"2026-04-07T11:49:11Z","scopus_import":"1","article_processing_charge":"No","article_type":"original"},{"publication_status":"published","doi":"10.1007/978-3-031-19803-8_21","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2208.03160"}],"corr_author":"1","abstract":[{"lang":"eng","text":"It is a highly desirable property for deep networks to be robust against\r\nsmall input changes. One popular way to achieve this property is by designing\r\nnetworks with a small Lipschitz constant. In this work, we propose a new\r\ntechnique for constructing such Lipschitz networks that has a number of\r\ndesirable properties: it can be applied to any linear network layer\r\n(fully-connected or convolutional), it provides formal guarantees on the\r\nLipschitz constant, it is easy to implement and efficient to run, and it can be\r\ncombined with any training objective and optimization method. In fact, our\r\ntechnique is the first one in the literature that achieves all of these\r\nproperties simultaneously. Our main contribution is a rescaling-based weight\r\nmatrix parametrization that guarantees each network layer to have a Lipschitz\r\nconstant of at most 1 and results in the learned weight matrices to be close to\r\northogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL).\r\nExperiments and ablation studies in the context of image classification with\r\ncertified robust accuracy confirm that AOL layers achieve results that are on\r\npar with most existing methods. Yet, they are simpler to implement and more\r\nbroadly applicable, because they do not require computationally expensive\r\nmatrix orthogonalization or inversion steps as part of the network\r\narchitecture. We provide code at https://github.com/berndprach/AOL."}],"language":[{"iso":"eng"}],"title":"Almost-orthogonal layers for efficient general-purpose Lipschitz networks","volume":13681,"alternative_title":["LNCS"],"year":"2022","day":"23","conference":{"start_date":"2022-10-23","location":"Tel Aviv, Israel","name":"ECCV: European Conference on Computer Vision","end_date":"2022-10-27"},"oa":1,"article_processing_charge":"No","scopus_import":"1","date_updated":"2026-04-07T11:49:51Z","publication":"Computer Vision – ECCV 2022","type":"conference","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19759"}]},"oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Prach, Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach","first_name":"Bernd"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph"}],"arxiv":1,"external_id":{"arxiv":["2208.03160"],"isi":["000904104000021"]},"isi":1,"page":"350-365","status":"public","month":"10","publisher":"Springer Nature","citation":{"ieee":"B. Prach and C. Lampert, “Almost-orthogonal layers for efficient general-purpose Lipschitz networks,” in <i>Computer Vision – ECCV 2022</i>, Tel Aviv, Israel, 2022, vol. 13681, pp. 350–365.","apa":"Prach, B., &#38; Lampert, C. (2022). Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In <i>Computer Vision – ECCV 2022</i> (Vol. 13681, pp. 350–365). Tel Aviv, Israel: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>","ama":"Prach B, Lampert C. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. In: <i>Computer Vision – ECCV 2022</i>. Vol 13681. Springer Nature; 2022:350-365. doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>","ista":"Prach B, Lampert C. 2022. Almost-orthogonal layers for efficient general-purpose Lipschitz networks. Computer Vision – ECCV 2022. ECCV: European Conference on Computer Vision, LNCS, vol. 13681, 350–365.","mla":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” <i>Computer Vision – ECCV 2022</i>, vol. 13681, Springer Nature, 2022, pp. 350–65, doi:<a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">10.1007/978-3-031-19803-8_21</a>.","short":"B. Prach, C. Lampert, in:, Computer Vision – ECCV 2022, Springer Nature, 2022, pp. 350–365.","chicago":"Prach, Bernd, and Christoph Lampert. “Almost-Orthogonal Layers for Efficient General-Purpose Lipschitz Networks.” In <i>Computer Vision – ECCV 2022</i>, 13681:350–65. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-19803-8_21\">https://doi.org/10.1007/978-3-031-19803-8_21</a>."},"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_created":"2022-08-12T15:09:47Z","intvolume":"     13681","publication_identifier":{"isbn":["9783031198021"],"eisbn":["9783031198038"]},"_id":"11839","date_published":"2022-10-23T00:00:00Z","quality_controlled":"1"},{"article_processing_charge":"No","article_type":"original","scopus_import":"1","publication":"Physical Review Materials","type":"journal_article","date_updated":"2026-04-07T11:50:54Z","doi":"10.1103/PhysRevMaterials.6.125605","publication_status":"published","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"ec_funded":1,"article_number":"125605","language":[{"iso":"eng"}],"abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"oa":1,"day":"29","year":"2022","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","volume":6,"month":"12","status":"public","date_created":"2023-01-08T23:00:53Z","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"citation":{"chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>.","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022.","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>"},"publisher":"American Physical Society","_id":"12109","publication_identifier":{"eissn":["2475-9953"]},"intvolume":"         6","issue":"12","project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"}],"quality_controlled":"1","date_published":"2022-12-29T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","related_material":{"record":[{"id":"20203","status":"public","relation":"dissertation_contains"}]},"isi":1,"external_id":{"arxiv":["2209.01889"],"isi":["000908384800001"]},"arxiv":1,"author":[{"last_name":"Pertl","first_name":"Felix","orcid":"0000-0003-0463-5794","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix"},{"full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A"},{"orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B","first_name":"Lubuna B","last_name":"Shafeek"},{"last_name":"Cramer","first_name":"Tobias","full_name":"Cramer, Tobias"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work."},{"oa":1,"day":"15","year":"2022","title":"A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation","volume":25,"article_number":"104580","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2022-07-04T08:19:25Z","ec_funded":1,"doi":"10.1016/j.isci.2022.104580","publication_status":"published","type":"journal_article","publication":"iScience","date_updated":"2026-04-07T11:51:43Z","scopus_import":"1","ddc":["610"],"article_processing_charge":"Yes","article_type":"original","file":[{"file_id":"11480","date_updated":"2022-07-04T08:19:25Z","creator":"cchlebak","content_type":"application/pdf","date_created":"2022-07-04T08:19:25Z","access_level":"open_access","relation":"main_file","file_name":"2022_iScience_Bartalska.pdf","file_size":19400048,"success":1,"checksum":"a470b74e1b3796c710189c81a4cd4329"}],"has_accepted_license":"1","acknowledgement":"We thank the scientific service units at ISTA, specifically the lab support facility and imaging & optics facility for their support; Nicolas Armel for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner for their help in human brain tissue collection, Rouven Schulz for his insights into the functional assays We thank all members of the Siegert group for constant feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for feedback on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","isi":1,"external_id":{"isi":["000830428500005"],"pmid":["35789843"]},"author":[{"last_name":"Bartalska","first_name":"Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87","full_name":"Bartalska, Katarina"},{"last_name":"Hübschmann","first_name":"Verena","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Medina","last_name":"Korkut","full_name":"Korkut, Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4309-2251"},{"orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","last_name":"Cubero","first_name":"Ryan J"},{"last_name":"Venturino","first_name":"Alessandro","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","last_name":"Rössler","full_name":"Rössler, Karl"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"first_name":"Sandra","last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","related_material":{"record":[{"relation":"other","status":"public","id":"12117"},{"relation":"dissertation_contains","id":"20074","status":"public"}]},"project":[{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017"}],"quality_controlled":"1","date_published":"2022-07-15T00:00:00Z","_id":"11478","publication_identifier":{"eissn":["2589-0042"]},"issue":"7","intvolume":"        25","department":[{"_id":"SaSi"}],"date_created":"2022-07-03T22:01:33Z","citation":{"ieee":"K. Bartalska <i>et al.</i>, “A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation,” <i>iScience</i>, vol. 25, no. 7. Elsevier, 2022.","ama":"Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>iScience</i>. 2022;25(7). doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>","apa":"Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler, K., … Siegert, S. (2022). A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>","short":"K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler, T. Czech, S. Siegert, IScience 25 (2022).","mla":"Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>, vol. 25, no. 7, 104580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>.","ista":"Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. iScience. 25(7), 104580.","chicago":"Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>."},"publisher":"Elsevier","month":"07","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"scopus_import":"1","ddc":["580"],"type":"journal_article","publication":"Nature","date_updated":"2026-04-07T11:52:15Z","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"oa":1,"day":"15","year":"2022","volume":609,"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","doi":"10.1038/s41586-022-05187-x","publication_status":"published","file_date_updated":"2023-11-02T17:12:37Z","ec_funded":1,"_id":"12291","intvolume":"       609","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"issue":"7927","quality_controlled":"1","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}],"date_published":"2022-09-15T00:00:00Z","month":"09","status":"public","page":"575-581","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"date_created":"2023-01-16T10:04:48Z","publisher":"Springer Nature","citation":{"ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>"},"file":[{"date_created":"2023-11-02T17:12:37Z","relation":"main_file","access_level":"open_access","checksum":"a6055c606aefb900bf62ae3e7d15f921","success":1,"file_size":79774945,"file_name":"Friml Nature 2022_merged.pdf","date_updated":"2023-11-02T17:12:37Z","file_id":"14483","creator":"amally","content_type":"application/pdf"}],"has_accepted_license":"1","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19395"},{"id":"20364","status":"public","relation":"dissertation_contains"}]},"isi":1,"external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C"},{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana","last_name":"Gelová"},{"first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge"},{"full_name":"Živanović, Branka D.","first_name":"Branka D.","last_name":"Živanović"},{"last_name":"Zou","first_name":"Minxia","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","full_name":"Fiedler, Lukas","last_name":"Fiedler","first_name":"Lukas"},{"first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones"},{"last_name":"Hrtyan","first_name":"Mónika","full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"full_name":"Kuhn, Andre","first_name":"Andre","last_name":"Kuhn"},{"orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","last_name":"Narasimhan"},{"last_name":"Randuch","first_name":"Marek","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova","first_name":"Anastasiia"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"}],"pmid":1},{"day":"01","oa":1,"title":"Impurity with a resonance in the vicinity of the Fermi energy","volume":4,"year":"2022","article_number":"013160","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We study an impurity with a resonance level whose position coincides with the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation of the scattering phase shift for fermions at the Fermi surface, introducing a new characteristic length scale into the problem. We investigate manifestations of this length scale in the self-energy of the impurity and in the density of the bath. Our calculations reveal a model-independent deformation of the density of the Fermi gas, which is determined by the width of the resonance. To provide a broader picture, we investigate time evolution of the density in quench dynamics, and study the behavior of the system at finite temperatures. Finally, we briefly discuss implications of our findings for the Fermi-polaron problem."}],"corr_author":"1","file_date_updated":"2022-03-14T08:38:49Z","ec_funded":1,"doi":"10.1103/PhysRevResearch.4.013160","publication_status":"published","date_updated":"2026-04-07T11:52:53Z","publication":"Physical Review Research","type":"journal_article","ddc":["530"],"scopus_import":"1","article_processing_charge":"No","article_type":"original","has_accepted_license":"1","acknowledgement":"M.L. acknowledges support by the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council (ERC) starting Grant No. 801770 (ANGULON). A.G.V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","file":[{"date_updated":"2022-03-14T08:38:49Z","file_id":"10848","creator":"dernst","content_type":"application/pdf","date_created":"2022-03-14T08:38:49Z","relation":"main_file","access_level":"open_access","file_size":1258324,"success":1,"checksum":"62f64b3421a969656ebf52467fa7b6e8","file_name":"2022_PhysicalReviewResearch_Maslov.pdf"}],"author":[{"full_name":"Maslov, Mikhail","orcid":"0000-0003-4074-2570","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Maslov"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail"},{"first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"arxiv":1,"external_id":{"arxiv":["2111.13570"]},"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","id":"19048","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"quality_controlled":"1","date_published":"2022-03-01T00:00:00Z","intvolume":"         4","publication_identifier":{"issn":["2643-1564"]},"_id":"10845","department":[{"_id":"MiLe"}],"date_created":"2022-03-13T23:01:46Z","citation":{"apa":"Maslov, M., Lemeshko, M., &#38; Volosniev, A. (2022). Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>","ama":"Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. 2022;4. doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>","ieee":"M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the vicinity of the Fermi energy,” <i>Physical Review Research</i>, vol. 4. American Physical Society, 2022.","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>.","ista":"Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 4, 013160.","mla":"Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>, vol. 4, 013160, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>.","short":"M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022)."},"publisher":"American Physical Society","status":"public","month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"article_number":"241","language":[{"iso":"eng"}],"abstract":[{"text":"This paper presents a new representation of curve dynamics, with applications to vortex filaments in fluid dynamics. Instead of representing these filaments with explicit curve geometry and Lagrangian equations of motion, we represent curves implicitly with a new co-dimensional 2 level set description. Our implicit representation admits several redundant mathematical degrees of freedom in both the configuration and the dynamics of the curves, which can be tailored specifically to improve numerical robustness, in contrast to naive approaches for implicit curve dynamics that suffer from overwhelming numerical stability problems. Furthermore, we note how these hidden degrees of freedom perfectly map to a Clebsch representation in fluid dynamics. Motivated by these observations, we introduce untwisted level set functions and non-swirling dynamics which successfully regularize sources of numerical instability, particularly in the twisting modes around curve filaments. A consequence is a novel simulation method which produces stable dynamics for large numbers of interacting vortex filaments and effortlessly handles topological changes and re-connection events.","lang":"eng"}],"oa":1,"day":"01","year":"2022","title":"Hidden degrees of freedom in implicit vortex filaments","volume":41,"doi":"10.1145/3550454.3555459","publication_status":"published","file_date_updated":"2023-01-30T07:15:48Z","scopus_import":"1","ddc":["000"],"type":"journal_article","publication":"ACM Transactions on Graphics","date_updated":"2026-04-07T12:02:23Z","article_processing_charge":"No","article_type":"original","file":[{"date_created":"2023-01-30T07:15:48Z","access_level":"open_access","relation":"main_file","file_name":"2022_ACM_Ishida.pdf","success":1,"file_size":15551202,"checksum":"a2fba257fdefe0e747182be6c0f7c70c","file_id":"12433","date_updated":"2023-01-30T07:15:48Z","creator":"dernst","content_type":"application/pdf"}],"has_accepted_license":"1","acknowledgement":"We thank the visual computing group at IST Austria for their valuable discussions and feedback. Houdini Education licenses were provided by SideFX software. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"dissertation_contains","id":"20551","status":"public"}]},"oa_version":"Published Version","isi":1,"external_id":{"isi":["000891651900061"]},"author":[{"last_name":"Ishida","first_name":"Sadashige","full_name":"Ishida, Sadashige","orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"},{"full_name":"Chern, Albert","first_name":"Albert","last_name":"Chern"}],"_id":"12431","intvolume":"        41","issue":"6","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"quality_controlled":"1","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"date_published":"2022-12-01T00:00:00Z","month":"12","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"ChWo"}],"date_created":"2023-01-29T23:00:59Z","publisher":"Association for Computing Machinery","citation":{"ama":"Ishida S, Wojtan C, Chern A. Hidden degrees of freedom in implicit vortex filaments. <i>ACM Transactions on Graphics</i>. 2022;41(6). doi:<a href=\"https://doi.org/10.1145/3550454.3555459\">10.1145/3550454.3555459</a>","apa":"Ishida, S., Wojtan, C., &#38; Chern, A. (2022). Hidden degrees of freedom in implicit vortex filaments. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3550454.3555459\">https://doi.org/10.1145/3550454.3555459</a>","ieee":"S. Ishida, C. Wojtan, and A. Chern, “Hidden degrees of freedom in implicit vortex filaments,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 6. Association for Computing Machinery, 2022.","chicago":"Ishida, Sadashige, Chris Wojtan, and Albert Chern. “Hidden Degrees of Freedom in Implicit Vortex Filaments.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3550454.3555459\">https://doi.org/10.1145/3550454.3555459</a>.","short":"S. Ishida, C. Wojtan, A. Chern, ACM Transactions on Graphics 41 (2022).","mla":"Ishida, Sadashige, et al. “Hidden Degrees of Freedom in Implicit Vortex Filaments.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 6, 241, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3550454.3555459\">10.1145/3550454.3555459</a>.","ista":"Ishida S, Wojtan C, Chern A. 2022. Hidden degrees of freedom in implicit vortex filaments. ACM Transactions on Graphics. 41(6), 241."}},{"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20147"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"author":[{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"external_id":{"isi":["000866539700011"]},"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","has_accepted_license":"1","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"12317","date_updated":"2023-01-20T07:34:50Z","file_name":"2022_LNCS_RV_Henzinger.pdf","file_size":477110,"checksum":"05c7dcfbb9053a98f46441fb2eccb213","success":1,"date_created":"2023-01-20T07:34:50Z","access_level":"open_access","relation":"main_file"}],"status":"public","month":"09","page":"200-220","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_created":"2022-08-08T17:09:09Z","citation":{"ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for quantitative specifications,” in <i>22nd International Conference on Runtime Verification</i>, Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2022). Abstract monitors for quantitative specifications. In <i>22nd International Conference on Runtime Verification</i> (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications. In: <i>22nd International Conference on Runtime Verification</i>. Vol 13498. Springer Nature; 2022:200-220. doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>","mla":"Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.” <i>22nd International Conference on Runtime Verification</i>, vol. 13498, Springer Nature, 2022, pp. 200–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference on Runtime Verification, Springer Nature, 2022, pp. 200–220.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative specifications. 22nd International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 13498, 200–220.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract Monitors for Quantitative Specifications.” In <i>22nd International Conference on Runtime Verification</i>, 13498:200–220. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>."},"publisher":"Springer Nature","intvolume":"     13498","publication_identifier":{"issn":["0302-9743"]},"_id":"11775","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"date_published":"2022-09-23T00:00:00Z","doi":"10.1007/978-3-031-17196-3_11","publication_status":"published","file_date_updated":"2023-01-20T07:34:50Z","ec_funded":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. "}],"corr_author":"1","conference":{"start_date":"2022-09-28","location":"Tbilisi, Georgia","end_date":"2022-09-30","name":"RV: Runtime Verification"},"day":"23","oa":1,"title":"Abstract monitors for quantitative specifications","volume":13498,"alternative_title":["LNCS"],"year":"2022","article_processing_charge":"Yes","ddc":["000"],"scopus_import":"1","date_updated":"2026-04-07T12:02:56Z","publication":"22nd International Conference on Runtime Verification","type":"conference"}]