[{"OA_place":"publisher","acknowledgement":"We acknowledge support from eRc project n-AQUA, grant agreement 101071937. B.c. acknowledges support from the nOMiS Foundation. M.L. acknowledges support from theAlexander von humboldt foundation. Q.Y. acknowledges support from the Royal SocietyUniversity Research Fellowship URF\\R1\\221096 and UK Research and innovation Grant (eP/X017575/1). ","DOAJ_listed":"1","supplementarymaterial":"yes","abstract":[{"text":"Mechanosensitive ion transport plays a central role in enabling living systems to perceive and adapt to their environment through the deformation of soft, embedded ion channels. In this work, we demonstrate that ion transport within a two-dimensional graphite nanoslit can be rationally engineered to achieve a bipolar, pressure-sensitive response without any structural deformation. The mechanosensitivity arises from the selective charging of one channel inlet, which acts as a reversible source of mobile charge carriers. These excess ions can then be advected in or out of the channel by the pressure-driven water flow, thereby modulating the ionic conductance. This mechanism is captured through a comprehensive electrohydrodynamic model that analytically accounts for coupled diffusion, convection, surface transport, diffusio-osmosis, and interfacial slippage, both inside and outside the nanoslit. The theoretical framework quantitatively reproduces the experimental data, showing that a simple surface charge pattern can give rise to complex, pressure-dependent conductance. These findings reveal how rich nonlinear couplings at the nanoscale can be harnessed to design adaptive, bioinspired nanofluidic systems, exemplified here by ionic pressure sensors.","lang":"eng"}],"year":"2026","dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. no new materials have been created for this work","status":"public","title":"Architecting mechanosensitive nanofluidic transport in graphite nanoslits","has_accepted_license":"1","publication_status":"published","file":[{"file_size":1264180,"date_updated":"2026-09-24T10:46:31Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2026-09-24T10:46:31Z","relation":"main_file","checksum":"ae3d6231ea5cea3a0014a6da2e8c8c30","file_name":"2026_ScienceAdv_Lizee.pdf","success":1,"file_id":"22989"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"22952","das_tickbox":"1","publication":"Science Advances","quality_controlled":"1","citation":{"ieee":"M. Lizée, Z. Zhang, B. Coquinot, Q. Yang, and L. Bocquet, “Architecting mechanosensitive nanofluidic transport in graphite nanoslits,” <i>Science Advances</i>, vol. 12, no. 31. AAAS, 2026.","ama":"Lizée M, Zhang Z, Coquinot B, Yang Q, Bocquet L. Architecting mechanosensitive nanofluidic transport in graphite nanoslits. <i>Science Advances</i>. 2026;12(31). doi:<a href=\"https://doi.org/10.1126/sciadv.aed4451\">10.1126/sciadv.aed4451</a>","apa":"Lizée, M., Zhang, Z., Coquinot, B., Yang, Q., &#38; Bocquet, L. (2026). Architecting mechanosensitive nanofluidic transport in graphite nanoslits. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.aed4451\">https://doi.org/10.1126/sciadv.aed4451</a>","chicago":"Lizée, Mathieu, Zhijia Zhang, Baptiste Coquinot, Qian Yang, and Lydéric Bocquet. “Architecting Mechanosensitive Nanofluidic Transport in Graphite Nanoslits.” <i>Science Advances</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/sciadv.aed4451\">https://doi.org/10.1126/sciadv.aed4451</a>.","mla":"Lizée, Mathieu, et al. “Architecting Mechanosensitive Nanofluidic Transport in Graphite Nanoslits.” <i>Science Advances</i>, vol. 12, no. 31, eaed4451, AAAS, 2026, doi:<a href=\"https://doi.org/10.1126/sciadv.aed4451\">10.1126/sciadv.aed4451</a>.","ista":"Lizée M, Zhang Z, Coquinot B, Yang Q, Bocquet L. 2026. Architecting mechanosensitive nanofluidic transport in graphite nanoslits. Science Advances. 12(31), eaed4451.","short":"M. Lizée, Z. Zhang, B. Coquinot, Q. Yang, L. Bocquet, Science Advances 12 (2026)."},"day":"01","external_id":{"pmid":["42525771"]},"publication_identifier":{"eissn":["2375-2548"]},"researchdata_availability":"no","date_published":"2026-07-01T00:00:00Z","doi":"10.1126/sciadv.aed4451","month":"07","type":"journal_article","PlanS_conform":"1","date_updated":"2026-09-24T12:00:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-17T11:05:47Z","article_type":"original","oa_version":"Published Version","publisher":"AAAS","pmid":1,"ddc":["530"],"file_date_updated":"2026-09-24T10:46:31Z","volume":12,"article_number":"eaed4451","scopus_import":"1","oa":1,"OA_type":"gold","department":[{"_id":"MiLe"}],"author":[{"full_name":"Lizée, Mathieu","last_name":"Lizée","first_name":"Mathieu"},{"first_name":"Zhijia","last_name":"Zhang","full_name":"Zhang, Zhijia"},{"last_name":"Coquinot","full_name":"Coquinot, Baptiste","orcid":"0000-0001-5524-596X","id":"f8417bd4-f599-11ee-a482-b927e3ed1e8e","first_name":"Baptiste"},{"full_name":"Yang, Qian","last_name":"Yang","first_name":"Qian"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"}],"article_processing_charge":"Yes","language":[{"iso":"eng"}],"intvolume":"        12","issue":"31","fulldoi":"https://doi.org/10.1126/sciadv.aed4451"},{"publication_status":"epub_ahead","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"22954","quality_controlled":"1","das_tickbox":"0","publication":"Journal of Dynamics and Differential Equations","day":"27","citation":{"chicago":"Baracco, Luca, Olga Bernardi, Anna Florio, and Alessandra Nardi. “Birkhoff Attractors for Dissipative Symplectic Billiards.” <i>Journal of Dynamics and Differential Equations</i>. Springer, 2026. <a href=\"https://doi.org/10.1007/s10884-026-10528-9\">https://doi.org/10.1007/s10884-026-10528-9</a>.","mla":"Baracco, Luca, et al. “Birkhoff Attractors for Dissipative Symplectic Billiards.” <i>Journal of Dynamics and Differential Equations</i>, Springer, 2026, doi:<a href=\"https://doi.org/10.1007/s10884-026-10528-9\">10.1007/s10884-026-10528-9</a>.","short":"L. Baracco, O. Bernardi, A. Florio, A. Nardi, Journal of Dynamics and Differential Equations (2026).","ista":"Baracco L, Bernardi O, Florio A, Nardi A. 2026. Birkhoff attractors for dissipative symplectic billiards. Journal of Dynamics and Differential Equations.","ieee":"L. Baracco, O. Bernardi, A. Florio, and A. Nardi, “Birkhoff attractors for dissipative symplectic billiards,” <i>Journal of Dynamics and Differential Equations</i>. Springer, 2026.","ama":"Baracco L, Bernardi O, Florio A, Nardi A. Birkhoff attractors for dissipative symplectic billiards. <i>Journal of Dynamics and Differential Equations</i>. 2026. doi:<a href=\"https://doi.org/10.1007/s10884-026-10528-9\">10.1007/s10884-026-10528-9</a>","apa":"Baracco, L., Bernardi, O., Florio, A., &#38; Nardi, A. (2026). Birkhoff attractors for dissipative symplectic billiards. <i>Journal of Dynamics and Differential Equations</i>. Springer. <a href=\"https://doi.org/10.1007/s10884-026-10528-9\">https://doi.org/10.1007/s10884-026-10528-9</a>"},"acknowledgement":"Open access funding provided by Università degli Studi di Padova within the CRUI-CARE Agreement. A.F. is partially supported by the ANR project CoSyDy (ANR-CE40-0014), the ANR project GALS (ANR-23-CE40-0001) and PEPS project “Jeuns chercheurs et jeunes chercheuses” 2025. L.B. and O.B. have been partially supported by the PRIN project 2022FPZEES “Stability in Hamiltonian Dynamics and Beyond”.","OA_place":"publisher","supplementarymaterial":"no","abstract":[{"text":"The aim of the present paper is to propose and study a dissipative variant of symplectic billiards within planar strictly convex domains. The associated billiard map is dissipative, thus it admits a compact invariant set, the so-called Birkhoff attractor. Its complexity depends on the rate of dissipation as well as on the geometry of the billiard table. We prove that (a) for strong dissipation, the Birkhoff attractor is a normally contracted graph over the zero section; (b) for mild dissipation, the Birkhoff attractor within a centrally symmetric domain is an indecomposable continuum whose restricted dynamics has positive topological entropy. We compare these results with those for dissipative Birkhoff billiards, studied in [15].","lang":"eng"}],"year":"2026","title":"Birkhoff attractors for dissipative symplectic billiards","status":"public","month":"07","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1007/s10884-026-10528-9","open_access":"1"}],"keyword":["Dissipative symplectic billiard","Birkhoff attractor","Conformally symplectic twist map"],"external_id":{"arxiv":["2509.13086"]},"publication_identifier":{"eissn":["1572-9222"],"issn":["1040-7294"]},"researchdata_availability":"no","date_published":"2026-07-27T00:00:00Z","doi":"10.1007/s10884-026-10528-9","arxiv":1,"article_type":"original","oa_version":"Published Version","publisher":"Springer","ddc":["500"],"PlanS_conform":"1","date_updated":"2026-09-24T12:26:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-17T11:05:59Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1007/s10884-026-10528-9","oa":1,"scopus_import":"1","author":[{"first_name":"Luca","last_name":"Baracco","full_name":"Baracco, Luca"},{"first_name":"Olga","last_name":"Bernardi","full_name":"Bernardi, Olga"},{"first_name":"Anna","last_name":"Florio","full_name":"Florio, Anna"},{"id":"3e9c89df-ff0c-11f0-9fd7-c11e36d36769","first_name":"Alessandra","last_name":"Nardi","full_name":"Nardi, Alessandra"}],"OA_type":"hybrid","department":[{"_id":"VaKa"}],"article_processing_charge":"Yes (via OA deal)"},{"citation":{"chicago":"Baracco, Luca, Olga Bernardi, and Alessandra Nardi. “Area Spectral Rigidity for Axially Symmetric Symplectic Billiard Tables.” <i>Journal of Modern Dynamics</i>. American Institute of Mathematical Sciences, 2026. <a href=\"https://doi.org/10.3934/jmd.2026012\">https://doi.org/10.3934/jmd.2026012</a>.","mla":"Baracco, Luca, et al. “Area Spectral Rigidity for Axially Symmetric Symplectic Billiard Tables.” <i>Journal of Modern Dynamics</i>, vol. 22, American Institute of Mathematical Sciences, 2026, pp. 469–88, doi:<a href=\"https://doi.org/10.3934/jmd.2026012\">10.3934/jmd.2026012</a>.","ista":"Baracco L, Bernardi O, Nardi A. 2026. Area spectral rigidity for axially symmetric symplectic billiard tables. Journal of Modern Dynamics. 22, 469–488.","short":"L. Baracco, O. Bernardi, A. Nardi, Journal of Modern Dynamics 22 (2026) 469–488.","ama":"Baracco L, Bernardi O, Nardi A. Area spectral rigidity for axially symmetric symplectic billiard tables. <i>Journal of Modern Dynamics</i>. 2026;22:469-488. doi:<a href=\"https://doi.org/10.3934/jmd.2026012\">10.3934/jmd.2026012</a>","ieee":"L. Baracco, O. Bernardi, and A. Nardi, “Area spectral rigidity for axially symmetric symplectic billiard tables,” <i>Journal of Modern Dynamics</i>, vol. 22. American Institute of Mathematical Sciences, pp. 469–488, 2026.","apa":"Baracco, L., Bernardi, O., &#38; Nardi, A. (2026). Area spectral rigidity for axially symmetric symplectic billiard tables. <i>Journal of Modern Dynamics</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/jmd.2026012\">https://doi.org/10.3934/jmd.2026012</a>"},"day":"24","publication":"Journal of Modern Dynamics","quality_controlled":"1","das_tickbox":"0","_id":"22953","publication_status":"published","title":"Area spectral rigidity for axially symmetric symplectic billiard tables","status":"public","corr_author":"1","abstract":[{"lang":"eng","text":"We prove that any finitely smooth, axially symmetric, strictly convex domain with everywhere positive curvature and sufficiently close to an ellipse is area spectrally rigid. This means that any area-isospectral family of domains in this class is necessarily equi-affine. We use techniques, adapted to symplectic billiards, inspired by the paper of J. De Simoi, V. Kaloshin and Q. Wei [5]."}],"year":"2026","supplementarymaterial":"no","OA_place":"repository","page":"469-488","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2410.12644"}],"type":"journal_article","month":"07","arxiv":1,"doi":"10.3934/jmd.2026012","date_published":"2026-07-24T00:00:00Z","researchdata_availability":"no","publication_identifier":{"eissn":["1930-532X"],"issn":["1930-5311"]},"external_id":{"arxiv":["2410.12644"]},"volume":22,"publisher":"American Institute of Mathematical Sciences","oa_version":"Preprint","article_type":"original","date_created":"2026-09-17T11:05:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-09-24T12:12:44Z","fulldoi":"https://doi.org/10.3934/jmd.2026012","intvolume":"        22","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Luca","last_name":"Baracco","full_name":"Baracco, Luca"},{"last_name":"Bernardi","full_name":"Bernardi, Olga","first_name":"Olga"},{"first_name":"Alessandra","id":"3e9c89df-ff0c-11f0-9fd7-c11e36d36769","full_name":"Nardi, Alessandra","last_name":"Nardi"}],"department":[{"_id":"VaKa"}],"OA_type":"green","scopus_import":"1","oa":1,"mathsc":["37D50","53C24","58J53"]},{"doi":"10.1016/j.cell.2026.06.009","date_published":"2026-08-20T00:00:00Z","external_id":{"pmid":["42379166"]},"keyword":["tissue patterning","heterogeneity","mechanics","intestinal regeneration","epigenetic competence","multiscale integration","modeling","organoids","image-based phenotyping","Yap1"],"researchdata_availability":"yes","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"type":"journal_article","page":"5266-5282.e17","ec_funded":1,"month":"08","year":"2026","abstract":[{"text":"Tissue regeneration requires de novo patterning, which has been proposed to be facilitated by cellular heterogeneity. Yet how such heterogeneities are integrated with the mechanochemical state of the tissue and stabilized at the chromatin level into stable, spatially organized fates remains poorly understood. Using in vivo mouse intestinal regeneration models and organoids, we identify a critical density regime that produces a permissive window for heterogeneity in the mechanosensor Yes-associated protein 1 (YAP1). We show that YAP1 heterogeneity is coupled to lineage-biased chromatin accessibility and is decoded through FOXA1, which integrates the permissive chromatin state to Delta-Notch supracellular feedback and lineage commitment. This circuit generates fate bistability and preserves a memory of transient YAP1 activity, thereby maintaining spatial patterning as tissues return to homeostasis after injury. Together, our findings establish a multiscale framework in which tissue-scale mechanics tune single-cell competence and, through FOXA1-mediated bistability, convert transient heterogeneity into stable and self-organized tissue architecture.","lang":"eng"}],"dataavailabilitystatement":"All sequencing data have been deposited at the Gene Expression Omnibus (GEO) under accession number GEO: GSE283662.\r\nAnalysis of imaging and sequencing data was developed in the Liberali lab and is available at https://github.com/LiberaliLab/symmetry-breaking-2026. Detailed information on the packages used is provided in the STAR Methods section.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","corr_author":"1","status":"public","title":"Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning","acknowledgement":"We thank the Liberali group, M. Verbeek, and C. Soneson for fruitful discussions; E. Tagliavini for IT support; J. Lüthi for Fractal support; H. Köhler for FACS sorting; T.O. Buchholz for help on cell segmentation; B. Treutlein and A. Xavier da Silveira dos Santos for help with library preparation of single-cell ATAC-seq; M. Garioni for help with mouse salivary organoids; M. Kahnwald for help with human intestinal organoids; M. Lütolf, M. Nikolaev, and O. Mitrofanova for providing material and initial training for microwell experiments; J. Tchorz and V. Orsini for intestinal tissue sections of the YAP1 activator experiment in homeostasis; R. Kageyama for DLL1-Venus-T2A-mCherry mice; J.-F. Spetz for technical assistance; C. Lambert and N. Accart for help with sample preparation; Claudia Flandoli for graphic design of schemes; and Zuzana Nascakova for the graphical abstract. We thank the Foundation Hubrecht Organoid Technology (now Foundation Hubrecht Organoid Biobank, https://www.hubrechtorganoidbiobank.org/) for the duodenal organoid line used in this study (HUB-04-A2-001). We thank C.P. Heisenberg, M. Lütolf, C. Tsiairis, J. Zaugg, G. D’Angelo, L. Giorgetti, S. Arber, and the Liberali group for reading the manuscript. C.S. was supported by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 660-2020) and the Human Frontier Science Program (HFSP) LT000746/2021-L. D.B.B. was supported by the NOMIS Foundation as a NOMIS fellow, an EMBO Postdoctoral Fellowship (ALTF 343-2022), and the Austrian Academy of Sciences through an APART-MINT Fellowship. B.S. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust (FC001159). This work received funding from ERC to E.H. (grant number 851288) and to P.L. (grant number 758617) and from SNSF (310030_208162 and SNSF ERC TMCG-3_223263).","OA_place":"publisher","supplementarymaterial":"yes","_id":"22956","publication":"Cell","quality_controlled":"1","das_tickbox":"1","day":"20","citation":{"ista":"Schwayer C, Barbiero S, Brückner D, Oost KC, Baader C, Repina NA, Kim J, Diaz OE, Uccelli I, Capolupo L, Meylan LC, Kalck V, Moos F, Suppinger S, Yang Q, Schnabl J, Kilik U, Bourdon M, Camp JG, Stockinger B, Ferrari A, Bühler M, Stadler MB, Hannezo EB, Liberali P. 2026. Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. Cell. 189(17), 5266–5282.e17.","short":"C. Schwayer, S. Barbiero, D. Brückner, K.C. Oost, C. Baader, N.A. Repina, J. Kim, O.E. Diaz, I. Uccelli, L. Capolupo, L.C. Meylan, V. Kalck, F. Moos, S. Suppinger, Q. Yang, J. Schnabl, U. Kilik, M. Bourdon, J.G. Camp, B. Stockinger, A. Ferrari, M. Bühler, M.B. Stadler, E.B. Hannezo, P. Liberali, Cell 189 (2026) 5266–5282.e17.","mla":"Schwayer, Cornelia, et al. “Multiscale Integration of Tissue and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” <i>Cell</i>, vol. 189, no. 17, Cell Press, 2026, p. 5266–5282.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">10.1016/j.cell.2026.06.009</a>.","chicago":"Schwayer, Cornelia, Silvia Barbiero, David Brückner, Koen C. Oost, Clara Baader, Nicole A. Repina, Jinse Kim, et al. “Multiscale Integration of Tissue and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” <i>Cell</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">https://doi.org/10.1016/j.cell.2026.06.009</a>.","apa":"Schwayer, C., Barbiero, S., Brückner, D., Oost, K. C., Baader, C., Repina, N. A., … Liberali, P. (2026). Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">https://doi.org/10.1016/j.cell.2026.06.009</a>","ama":"Schwayer C, Barbiero S, Brückner D, et al. Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. <i>Cell</i>. 2026;189(17):5266-5282.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">10.1016/j.cell.2026.06.009</a>","ieee":"C. Schwayer <i>et al.</i>, “Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning,” <i>Cell</i>, vol. 189, no. 17. Cell Press, p. 5266–5282.e17, 2026."},"publication_status":"published","has_accepted_license":"1","file":[{"file_size":15536364,"date_updated":"2026-10-01T08:34:11Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2026-10-01T08:34:11Z","relation":"main_file","checksum":"3ff0f4f8be0e79940ba11b18af318ae3","file_name":"2026_Cell_Schwayer.pdf","success":1,"file_id":"23014"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"oa":1,"scopus_import":"1","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Schwayer, Cornelia","last_name":"Schwayer","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226"},{"full_name":"Barbiero, Silvia","last_name":"Barbiero","first_name":"Silvia"},{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","last_name":"Brückner"},{"last_name":"Oost","full_name":"Oost, Koen C.","first_name":"Koen C."},{"full_name":"Baader, Clara","last_name":"Baader","first_name":"Clara"},{"last_name":"Repina","full_name":"Repina, Nicole A.","first_name":"Nicole A."},{"last_name":"Kim","full_name":"Kim, Jinse","first_name":"Jinse"},{"first_name":"Oscar E.","last_name":"Diaz","full_name":"Diaz, Oscar E."},{"full_name":"Uccelli, Isa","last_name":"Uccelli","first_name":"Isa"},{"last_name":"Capolupo","full_name":"Capolupo, Laura","first_name":"Laura"},{"first_name":"Ludivine Challet","last_name":"Meylan","full_name":"Meylan, Ludivine Challet"},{"full_name":"Kalck, Veronique","last_name":"Kalck","first_name":"Veronique"},{"first_name":"Franziska","last_name":"Moos","full_name":"Moos, Franziska"},{"first_name":"Simon","full_name":"Suppinger, Simon","last_name":"Suppinger"},{"full_name":"Yang, Qiutan","last_name":"Yang","first_name":"Qiutan"},{"last_name":"Schnabl","full_name":"Schnabl, Jakob","first_name":"Jakob"},{"first_name":"Umut","full_name":"Kilik, Umut","last_name":"Kilik"},{"full_name":"Bourdon, Matthieu","last_name":"Bourdon","first_name":"Matthieu"},{"first_name":"J. Gray","full_name":"Camp, J. Gray","last_name":"Camp"},{"full_name":"Stockinger, Brigitta","last_name":"Stockinger","first_name":"Brigitta"},{"full_name":"Ferrari, Alessandra","last_name":"Ferrari","first_name":"Alessandra"},{"first_name":"Marc","last_name":"Bühler","full_name":"Bühler, Marc"},{"last_name":"Stadler","full_name":"Stadler, Michael B.","first_name":"Michael B."},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Liberali","full_name":"Liberali, Prisca","first_name":"Prisca"}],"issue":"17","intvolume":"       189","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"fulldoi":"https://doi.org/10.1016/j.cell.2026.06.009","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-17T11:06:12Z","date_updated":"2026-10-01T08:42:00Z","ddc":["570"],"file_date_updated":"2026-10-01T08:34:11Z","volume":189,"article_type":"original","oa_version":"Published Version","pmid":1,"publisher":"Cell Press"},{"acknowledgement":"We acknowledge the sponsors who made the SEH2Bioinfo possible, the organizers from the various Spanish-speaking RSGs, and\r\nthe collaborators who contributed to dissemination, logistics,\r\nand other essential tasks for its execution. G.J.O.-O. thanks the\r\nFONDECYT Postdoctoral Project No. 3250793 for financial support. G.J.O.-O. also expresses gratitude to Valentina Luza: “May\r\nher passion for science communication keep inspiring new generations, myself included, to infinity and beyond!” R.G.P.\r\nthanks the Argentinian public university education system as an\r\nelement of social ascendance and democratization of professional opportunities.","OA_place":"publisher","DOAJ_listed":"1","supplementarymaterial":"no","dataavailabilitystatement":"The data underlying this article, including the abstract books for\r\nthe first and second editions of the SEH2Bioinfo symposia, are\r\navailable in Zenodo at https://doi.org/10.5281/zenodo.6603621\r\nand https://doi.org/10.5281/zenodo.1,54,46,570, respectively.","abstract":[{"lang":"eng","text":"Linguistic inequality remains a silent barrier in contemporary science, particularly in rapidly evolving and interdisciplinary fields such as bioinformatics. This article examines how the Spanish-speaking community has responded to this gap through the creation of the Simposio de Estudiantes Hispanohablantes de Bioinformática y Biología Computacional (SEH2Bioinfo), a collective initiative that transforms language into a tool for inclusion and collaboration. Drawing on a historical review of the use of Spanish in scientific communication and an analysis of the two editions of SEH2Bioinfo (2022 and 2025), complemented by surveys of more than 1500 participants, we explore the effects of language on confidence, participation, and academic visibility. The findings show that Spanish can serve as a space for training and mentorship without compromising rigor, while simultaneously strengthening international networks and promoting open science. The growth of SEH2Bioinfo, its collaborative approach, and its intercontinental reach establish the symposium as a model for linguistic equity in scientific practice. Its experience demonstrates that expanding linguistic diversity in bioinformatics is not only possible but essential to building a global scientific community that is fairer, more connected, and representative."}],"year":"2026","title":"Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo","status":"public","publication_status":"published","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":1359968,"date_updated":"2026-10-01T08:55:00Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2026-10-01T08:55:00Z","relation":"main_file","checksum":"8885b0531a655103c46899b2f935b0db","file_name":"2026_BioinformaticsAdvances_Franzotti.pdf","success":1,"file_id":"23016"}],"_id":"22957","citation":{"ista":"Padilla Franzotti CL, Olguín-Orellana GJ, Palopoli N, Urquiza-Zurich S, Garcia-Moreno A, Monzón S, Cabrera-Pasadas M, Soler Sáez I, Perpiñá-Clérigues C, Puche Quiñonez RJ, Vélez Segura J, Lovaco-Flores JA, Osorio Mogollón CM, Esquinas-Román EM, Miserendino MC, Eranti P, Castillo-Orozco A, Cuesta-Astroz Y, Parra RG. 2026. Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo. Bioinformatics Advances. 6(1), vbag182.","short":"C.L. Padilla Franzotti, G.J. Olguín-Orellana, N. Palopoli, S. Urquiza-Zurich, A. Garcia-Moreno, S. Monzón, M. Cabrera-Pasadas, I. Soler Sáez, C. Perpiñá-Clérigues, R.J. Puche Quiñonez, J. Vélez Segura, J.A. Lovaco-Flores, C.M. Osorio Mogollón, E.M. Esquinas-Román, M.C. Miserendino, P. Eranti, A. Castillo-Orozco, Y. Cuesta-Astroz, R.G. Parra, Bioinformatics Advances 6 (2026).","chicago":"Padilla Franzotti, Carla L, Gabriel J Olguín-Orellana, Nicolas Palopoli, Sebastián Urquiza-Zurich, Adrian Garcia-Moreno, Sara Monzón, Mónica Cabrera-Pasadas, et al. “Bioinformatics in Español: Expanding Open, Diverse, and Collaborative Science through SEH2Bioinfo.” <i>Bioinformatics Advances</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/bioadv/vbag182\">https://doi.org/10.1093/bioadv/vbag182</a>.","mla":"Padilla Franzotti, Carla L., et al. “Bioinformatics in Español: Expanding Open, Diverse, and Collaborative Science through SEH2Bioinfo.” <i>Bioinformatics Advances</i>, vol. 6, no. 1, vbag182, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/bioadv/vbag182\">10.1093/bioadv/vbag182</a>.","apa":"Padilla Franzotti, C. L., Olguín-Orellana, G. J., Palopoli, N., Urquiza-Zurich, S., Garcia-Moreno, A., Monzón, S., … Parra, R. G. (2026). Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo. <i>Bioinformatics Advances</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioadv/vbag182\">https://doi.org/10.1093/bioadv/vbag182</a>","ieee":"C. L. Padilla Franzotti <i>et al.</i>, “Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo,” <i>Bioinformatics Advances</i>, vol. 6, no. 1. Oxford University Press, 2026.","ama":"Padilla Franzotti CL, Olguín-Orellana GJ, Palopoli N, et al. Bioinformatics in Español: Expanding open, diverse, and collaborative science through SEH2Bioinfo. <i>Bioinformatics Advances</i>. 2026;6(1). doi:<a href=\"https://doi.org/10.1093/bioadv/vbag182\">10.1093/bioadv/vbag182</a>"},"day":"06","publication":"Bioinformatics Advances","quality_controlled":"1","das_tickbox":"1","external_id":{"pmid":["42577783"]},"publication_identifier":{"eissn":["2635-0041"]},"researchdata_availability":"yes","date_published":"2026-08-06T00:00:00Z","doi":"10.1093/bioadv/vbag182","month":"08","type":"journal_article","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/bioadv/vbag271"}]},"date_updated":"2026-10-01T08:59:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-17T11:06:17Z","oa_version":"Published Version","article_type":"original","publisher":"Oxford University Press","pmid":1,"file_date_updated":"2026-10-01T08:55:00Z","ddc":["570"],"volume":6,"article_number":"vbag182","oa":1,"scopus_import":"1","author":[{"last_name":"Padilla Franzotti","full_name":"Padilla Franzotti, Carla L","first_name":"Carla L"},{"full_name":"Olguín-Orellana, Gabriel J","last_name":"Olguín-Orellana","first_name":"Gabriel J"},{"full_name":"Palopoli, Nicolas","last_name":"Palopoli","first_name":"Nicolas"},{"full_name":"Urquiza-Zurich, Sebastián","last_name":"Urquiza-Zurich","first_name":"Sebastián"},{"first_name":"Adrian","last_name":"Garcia-Moreno","full_name":"Garcia-Moreno, Adrian"},{"first_name":"Sara","last_name":"Monzón","full_name":"Monzón, Sara"},{"first_name":"Mónica","full_name":"Cabrera-Pasadas, Mónica","last_name":"Cabrera-Pasadas"},{"full_name":"Soler Sáez, Irene","last_name":"Soler Sáez","first_name":"Irene"},{"last_name":"Perpiñá-Clérigues","full_name":"Perpiñá-Clérigues, Carla","first_name":"Carla"},{"first_name":"Rafael J","full_name":"Puche Quiñonez, Rafael J","last_name":"Puche Quiñonez"},{"first_name":"Jennifer","last_name":"Vélez Segura","full_name":"Vélez Segura, Jennifer"},{"last_name":"Lovaco-Flores","full_name":"Lovaco-Flores, Jose Abel","first_name":"Jose Abel"},{"full_name":"Osorio Mogollón, Cleidy M","last_name":"Osorio Mogollón","first_name":"Cleidy M"},{"first_name":"Eva M","full_name":"Esquinas-Román, Eva M","last_name":"Esquinas-Román"},{"full_name":"Miserendino, Maria C","last_name":"Miserendino","first_name":"Maria C","id":"273e0cbd-72f0-11ef-b75a-f9f932e292fa"},{"full_name":"Eranti, Pradeep","last_name":"Eranti","first_name":"Pradeep"},{"first_name":"Ana","last_name":"Castillo-Orozco","full_name":"Castillo-Orozco, Ana"},{"last_name":"Cuesta-Astroz","full_name":"Cuesta-Astroz, Yesid","first_name":"Yesid"},{"first_name":"R Gonzalo","full_name":"Parra, R Gonzalo","last_name":"Parra"}],"article_processing_charge":"Yes","OA_type":"gold","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"intvolume":"         6","issue":"1","fulldoi":"https://doi.org/10.1093/bioadv/vbag182"},{"article_number":"084505","oa":1,"scopus_import":"1","author":[{"first_name":"Marta M","id":"fdac3bd4-d1c1-11ef-aaa4-fad05dc21577","full_name":"Marchese, Marta M","last_name":"Marchese"},{"full_name":"Braun, Daniel","last_name":"Braun","first_name":"Daniel"},{"last_name":"Nimmrichter","full_name":"Nimmrichter, Stefan","first_name":"Stefan"},{"full_name":"Rätzel, Dennis","last_name":"Rätzel","first_name":"Dennis"}],"OA_type":"gold","department":[{"_id":"OnHo"}],"article_processing_charge":"Yes","language":[{"iso":"eng"}],"issue":"8","intvolume":"        28","fulldoi":"https://doi.org/10.1088/1367-2630/ae8b16","project":[{"grant_number":"COE01","name":"Quantum Science Austria (Hosten)","_id":"3b79db15-b029-11f1-a721-dbd41d892ec2"}],"date_updated":"2026-10-01T09:19:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-17T11:06:23Z","article_type":"original","oa_version":"Published Version","publisher":"IOP Publishing","file_date_updated":"2026-10-01T09:17:19Z","ddc":["530"],"volume":28,"external_id":{"arxiv":["2602.08981"]},"publication_identifier":{"eissn":["1367-2630"]},"researchdata_availability":"no","date_published":"2026-08-13T00:00:00Z","doi":"10.1088/1367-2630/ae8b16","arxiv":1,"month":"08","type":"journal_article","acknowledgement":"We thank Germain Tobar, Navdeep Arya, Magdalena Zych, Teodor Strömberg and Onur Hosten for useful discussions. M M M acknowledges support from the Walter Benjamin Programme (Project Number 510053905) and from the Austrian Science Fund (FWF) [10.55776/COE1]. DB acknowledges funding by the EU EIC Pathfinder project QuCoM (101046973). D R acknowledges funding by the Federal Ministry of Education and Research of Germany in the project ‘Open6GHub’ (Grant Number: 16KISK016), financial support from EPSRC (Engineering & Physical Sciences Research Council, United Kingdom) Grant Number EP/X009467/1, and support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2123 QuantumFrontiers - 390837967.","OA_place":"publisher","DOAJ_listed":"1","supplementarymaterial":"yes","abstract":[{"text":"We propose a sensing scheme for detecting weak forces that achieves sensitivity scaling proportional to the number of individual sensors without relying on entanglement or other non-classical resources. Our scheme utilizes coherent averaging across a chain of \r\n optomechanical cavities, unidirectionally coupled via a laser beam. As the beam passes through the cavities, it accumulates phase shifts induced by a common external force acting on the mechanical elements. Remarkably, this fully classical approach achieves the sensitivity scaling typically associated with quantum-enhanced protocols, providing a robust and experimentally feasible route to precision sensing. Potential applications range from high-sensitivity gravitational field measurements at the Large Hadron Collider to probing dark matter interactions and detecting gravitational waves. This work opens a new pathway for leveraging coherent light-matter interactions for force sensing.","lang":"eng"}],"year":"2026","dataavailabilitystatement":"All data that support the findings of this study are included within the article (and any supplementary files).","corr_author":"1","status":"public","title":"Cascaded optomechanical sensing for small signals","has_accepted_license":"1","publication_status":"published","file":[{"relation":"main_file","checksum":"b932d9f4bac1a2f6777e41d884b7b703","file_name":"2026_NewJourPhysics_Marchese.pdf","success":1,"file_id":"23018","file_size":799610,"date_updated":"2026-10-01T09:17:19Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2026-10-01T09:17:19Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"22958","publication":"New Journal of Physics","quality_controlled":"1","das_tickbox":"1","citation":{"ista":"Marchese MM, Braun D, Nimmrichter S, Rätzel D. 2026. Cascaded optomechanical sensing for small signals. New Journal of Physics. 28(8), 084505.","short":"M.M. Marchese, D. Braun, S. Nimmrichter, D. Rätzel, New Journal of Physics 28 (2026).","mla":"Marchese, Marta M., et al. “Cascaded Optomechanical Sensing for Small Signals.” <i>New Journal of Physics</i>, vol. 28, no. 8, 084505, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.1088/1367-2630/ae8b16\">10.1088/1367-2630/ae8b16</a>.","chicago":"Marchese, Marta M, Daniel Braun, Stefan Nimmrichter, and Dennis Rätzel. “Cascaded Optomechanical Sensing for Small Signals.” <i>New Journal of Physics</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.1088/1367-2630/ae8b16\">https://doi.org/10.1088/1367-2630/ae8b16</a>.","apa":"Marchese, M. M., Braun, D., Nimmrichter, S., &#38; Rätzel, D. (2026). Cascaded optomechanical sensing for small signals. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ae8b16\">https://doi.org/10.1088/1367-2630/ae8b16</a>","ieee":"M. M. Marchese, D. Braun, S. Nimmrichter, and D. Rätzel, “Cascaded optomechanical sensing for small signals,” <i>New Journal of Physics</i>, vol. 28, no. 8. IOP Publishing, 2026.","ama":"Marchese MM, Braun D, Nimmrichter S, Rätzel D. Cascaded optomechanical sensing for small signals. <i>New Journal of Physics</i>. 2026;28(8). doi:<a href=\"https://doi.org/10.1088/1367-2630/ae8b16\">10.1088/1367-2630/ae8b16</a>"},"day":"13"},{"publisher":"Oxford University Press","pmid":1,"oa_version":"Published Version","article_type":"review","volume":39,"file_date_updated":"2026-10-01T09:24:22Z","ddc":["570"],"date_updated":"2026-10-01T09:29:15Z","date_created":"2026-09-17T11:06:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1093/protein/gzag020","intvolume":"        39","article_number":"gzag020","department":[{"_id":"JuRe"}],"author":[{"full_name":"Ai, Hui-wang","last_name":"Ai","first_name":"Hui-wang"},{"first_name":"Frances H","full_name":"Arnold, Frances H","last_name":"Arnold"},{"last_name":"Barrick","full_name":"Barrick, Doug","first_name":"Doug"},{"first_name":"Hagan","full_name":"Bayley, Hagan","last_name":"Bayley"},{"first_name":"Alfie-Louise R","last_name":"Brownless","full_name":"Brownless, Alfie-Louise R"},{"last_name":"Campbell","full_name":"Campbell, Robert E","first_name":"Robert E"},{"first_name":"Roger","last_name":"Castells-Graells","full_name":"Castells-Graells, Roger"},{"first_name":"Pimchai","last_name":"Chaiyen","full_name":"Chaiyen, Pimchai"},{"first_name":"Roberto A","last_name":"Chica","full_name":"Chica, Roberto A"},{"full_name":"Chisholm, Lauren O","last_name":"Chisholm","first_name":"Lauren O"},{"first_name":"Daniel","full_name":"Christ, Daniel","last_name":"Christ"},{"first_name":"Guo-Chao","last_name":"Chu","full_name":"Chu, Guo-Chao"},{"first_name":"Michael","last_name":"Chungyoun","full_name":"Chungyoun, Michael"},{"first_name":"Vincent G H","last_name":"Eijsink","full_name":"Eijsink, Vincent G H"},{"first_name":"Michael B","last_name":"Elowitz","full_name":"Elowitz, Michael B"},{"first_name":"Douglas J","full_name":"Fansher, Douglas J","last_name":"Fansher"},{"last_name":"Fasan","full_name":"Fasan, Rudi","first_name":"Rudi"},{"first_name":"Gabriel","full_name":"Foley, Gabriel","last_name":"Foley"},{"first_name":"Michelle S","last_name":"Frei","full_name":"Frei, Michelle S"},{"first_name":"Andreas","last_name":"Gagsteiger","full_name":"Gagsteiger, Andreas"},{"first_name":"Ruiyan","full_name":"Gao, Ruiyan","last_name":"Gao"},{"full_name":"Gillam, Elizabeth M J","last_name":"Gillam","first_name":"Elizabeth M J"},{"last_name":"Gray","full_name":"Gray, Jeffrey J","first_name":"Jeffrey J"},{"full_name":"Guerra, Luis F","last_name":"Guerra","first_name":"Luis F"},{"full_name":"Höcker, Birte","last_name":"Höcker","first_name":"Birte"},{"first_name":"Zhiyang","full_name":"Jin, Zhiyang","last_name":"Jin"},{"full_name":"Kamerlin, Shina Caroline Lynn","last_name":"Kamerlin","first_name":"Shina Caroline Lynn"},{"last_name":"Koga","full_name":"Koga, Nobuyasu","first_name":"Nobuyasu"},{"full_name":"Kontermann, Roland E","last_name":"Kontermann","first_name":"Roland E"},{"full_name":"Kuhlman, Brian","last_name":"Kuhlman","first_name":"Brian"},{"full_name":"Langlois, Olivia A","last_name":"Langlois","first_name":"Olivia A"},{"first_name":"Dongyang","full_name":"Li, Dongyang","last_name":"Li"},{"full_name":"Lins, Roberto D","last_name":"Lins","first_name":"Roberto D"},{"full_name":"Liu, Chang C","last_name":"Liu","first_name":"Chang C"},{"first_name":"Lei","last_name":"Liu","full_name":"Liu, Lei"},{"last_name":"López Barreiro","full_name":"López Barreiro, Diego","first_name":"Diego"},{"first_name":"Peilong","full_name":"Lu, Peilong","last_name":"Lu"},{"full_name":"Mehta, Sohum","last_name":"Mehta","first_name":"Sohum"},{"first_name":"Ikumi","full_name":"Miyazaki, Ikumi","last_name":"Miyazaki"},{"last_name":"Müller","full_name":"Müller, Manuel M","first_name":"Manuel M"},{"first_name":"Serge","last_name":"Muyldermans","full_name":"Muyldermans, Serge"},{"last_name":"Nemoto","full_name":"Nemoto, Naoto","first_name":"Naoto"},{"full_name":"Nivala, Jeff","last_name":"Nivala","first_name":"Jeff"},{"last_name":"Nuñez","full_name":"Nuñez, James K","first_name":"James K"},{"first_name":"Izaiah J","full_name":"Ornelas, Izaiah J","last_name":"Ornelas"},{"first_name":"Joelle N","last_name":"Pelletier","full_name":"Pelletier, Joelle N"},{"full_name":"Plückthun, Andreas","last_name":"Plückthun","first_name":"Andreas"},{"last_name":"Porth","full_name":"Porth, Owen T","first_name":"Owen T"},{"last_name":"Prakinee","full_name":"Prakinee, Kridsadakorn","first_name":"Kridsadakorn"},{"full_name":"Qing, Yujia","last_name":"Qing","first_name":"Yujia"},{"id":"51d862e9-36ee-11f0-86d3-8534c85a5496","first_name":"Julia","last_name":"Reisenbauer","full_name":"Reisenbauer, Julia"},{"last_name":"Schmidt","full_name":"Schmidt, Sandy","first_name":"Sandy"},{"first_name":"Oliver","last_name":"Seifert","full_name":"Seifert, Oliver"},{"first_name":"Mikhail G","full_name":"Shapiro, Mikhail G","last_name":"Shapiro"},{"full_name":"Sharma, Rachna","last_name":"Sharma","first_name":"Rachna"},{"first_name":"Nilmani","full_name":"Singh, Nilmani","last_name":"Singh"},{"first_name":"Benjamin J","last_name":"Smith","full_name":"Smith, Benjamin J"},{"last_name":"Spangler","full_name":"Spangler, Jamie B","first_name":"Jamie B"},{"full_name":"Tatsumi-Koga, Rie","last_name":"Tatsumi-Koga","first_name":"Rie"},{"last_name":"Terai","full_name":"Terai, Takuya","first_name":"Takuya"},{"first_name":"Henrik","last_name":"Terholsen","full_name":"Terholsen, Henrik"},{"full_name":"Tolhurst, Mattias","last_name":"Tolhurst","first_name":"Mattias"},{"last_name":"Tripp","full_name":"Tripp, Katherine W","first_name":"Katherine W"},{"full_name":"Trossmann, Vanessa Tanja","last_name":"Trossmann","first_name":"Vanessa Tanja"},{"full_name":"Tucker, Chandra L","last_name":"Tucker","first_name":"Chandra L"},{"full_name":"Turak, Onur","last_name":"Turak","first_name":"Onur"},{"first_name":"James A","last_name":"Van Deventer","full_name":"Van Deventer, James A"},{"first_name":"Anikó","last_name":"Várnai","full_name":"Várnai, Anikó"},{"first_name":"Isabelle F T","full_name":"Viana, Isabelle F T","last_name":"Viana"},{"last_name":"Weeks","full_name":"Weeks, Amy M","first_name":"Amy M"},{"first_name":"K Dane","full_name":"Wittrup, K Dane","last_name":"Wittrup"},{"first_name":"Kingsley L-J","last_name":"Wong","full_name":"Wong, Kingsley L-J"},{"last_name":"Xi","full_name":"Xi, Chenggang","first_name":"Chenggang"},{"first_name":"Todd O","last_name":"Yeates","full_name":"Yeates, Todd O"},{"first_name":"Andy Hsien-Wei","full_name":"Yeh, Andy Hsien-Wei","last_name":"Yeh"},{"first_name":"Jin","last_name":"Zhang","full_name":"Zhang, Jin"},{"full_name":"Zhang, Tiger S","last_name":"Zhang","first_name":"Tiger S"},{"last_name":"Zhao","full_name":"Zhao, Huimin","first_name":"Huimin"},{"last_name":"Zheng","full_name":"Zheng, Fang","first_name":"Fang"},{"first_name":"Jingyi","last_name":"Zhu","full_name":"Zhu, Jingyi"},{"full_name":"Zinn, Sacha","last_name":"Zinn","first_name":"Sacha"}],"article_processing_charge":"No","OA_type":"hybrid","oa":1,"scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"4015ecfe11b3b0cac757d5bdd10d3c1d","relation":"main_file","file_id":"23019","success":1,"file_name":"2026_ProteinEngineeringDesignSelection_Ai.pdf","date_updated":"2026-10-01T09:24:22Z","file_size":12603911,"date_created":"2026-10-01T09:24:22Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf"}],"publication_status":"published","has_accepted_license":"1","day":"17","citation":{"mla":"Ai, Hui-wang, et al. “Protein Engineering: Status Report.” <i>Protein Engineering, Design and Selection</i>, vol. 39, gzag020, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/protein/gzag020\">10.1093/protein/gzag020</a>.","chicago":"Ai, Hui-wang, Frances H Arnold, Doug Barrick, Hagan Bayley, Alfie-Louise R Brownless, Robert E Campbell, Roger Castells-Graells, et al. “Protein Engineering: Status Report.” <i>Protein Engineering, Design and Selection</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/protein/gzag020\">https://doi.org/10.1093/protein/gzag020</a>.","short":"H. Ai, F.H. Arnold, D. Barrick, H. Bayley, A.-L.R. Brownless, R.E. Campbell, R. Castells-Graells, P. Chaiyen, R.A. Chica, L.O. Chisholm, D. Christ, G.-C. Chu, M. Chungyoun, V.G.H. Eijsink, M.B. Elowitz, D.J. Fansher, R. Fasan, G. Foley, M.S. Frei, A. Gagsteiger, R. Gao, E.M.J. Gillam, J.J. Gray, L.F. Guerra, B. Höcker, Z. Jin, S.C.L. Kamerlin, N. Koga, R.E. Kontermann, B. Kuhlman, O.A. Langlois, D. Li, R.D. Lins, C.C. Liu, L. Liu, D. López Barreiro, P. Lu, S. Mehta, I. Miyazaki, M.M. Müller, S. Muyldermans, N. Nemoto, J. Nivala, J.K. Nuñez, I.J. Ornelas, J.N. Pelletier, A. Plückthun, O.T. Porth, K. Prakinee, Y. Qing, J. Reisenbauer, S. Schmidt, O. Seifert, M.G. Shapiro, R. Sharma, N. Singh, B.J. Smith, J.B. Spangler, R. Tatsumi-Koga, T. Terai, H. Terholsen, M. Tolhurst, K.W. Tripp, V.T. Trossmann, C.L. Tucker, O. Turak, J.A. Van Deventer, A. Várnai, I.F.T. Viana, A.M. Weeks, K.D. Wittrup, K.L.-J. Wong, C. Xi, T.O. Yeates, A.H.-W. Yeh, J. Zhang, T.S. Zhang, H. Zhao, F. Zheng, J. Zhu, S. Zinn, Protein Engineering, Design and Selection 39 (2026).","ista":"Ai H, Arnold FH, Barrick D, Bayley H, Brownless A-LR, Campbell RE, Castells-Graells R, Chaiyen P, Chica RA, Chisholm LO, Christ D, Chu G-C, Chungyoun M, Eijsink VGH, Elowitz MB, Fansher DJ, Fasan R, Foley G, Frei MS, Gagsteiger A, Gao R, Gillam EMJ, Gray JJ, Guerra LF, Höcker B, Jin Z, Kamerlin SCL, Koga N, Kontermann RE, Kuhlman B, Langlois OA, Li D, Lins RD, Liu CC, Liu L, López Barreiro D, Lu P, Mehta S, Miyazaki I, Müller MM, Muyldermans S, Nemoto N, Nivala J, Nuñez JK, Ornelas IJ, Pelletier JN, Plückthun A, Porth OT, Prakinee K, Qing Y, Reisenbauer J, Schmidt S, Seifert O, Shapiro MG, Sharma R, Singh N, Smith BJ, Spangler JB, Tatsumi-Koga R, Terai T, Terholsen H, Tolhurst M, Tripp KW, Trossmann VT, Tucker CL, Turak O, Van Deventer JA, Várnai A, Viana IFT, Weeks AM, Wittrup KD, Wong KL-J, Xi C, Yeates TO, Yeh AH-W, Zhang J, Zhang TS, Zhao H, Zheng F, Zhu J, Zinn S. 2026. Protein engineering: Status report. Protein Engineering, Design and Selection. 39, gzag020.","ieee":"H. Ai <i>et al.</i>, “Protein engineering: Status report,” <i>Protein Engineering, Design and Selection</i>, vol. 39. Oxford University Press, 2026.","ama":"Ai H, Arnold FH, Barrick D, et al. Protein engineering: Status report. <i>Protein Engineering, Design and Selection</i>. 2026;39. doi:<a href=\"https://doi.org/10.1093/protein/gzag020\">10.1093/protein/gzag020</a>","apa":"Ai, H., Arnold, F. H., Barrick, D., Bayley, H., Brownless, A.-L. R., Campbell, R. E., … Zinn, S. (2026). Protein engineering: Status report. <i>Protein Engineering, Design and Selection</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/protein/gzag020\">https://doi.org/10.1093/protein/gzag020</a>"},"publication":"Protein Engineering, Design and Selection","quality_controlled":"1","das_tickbox":"1","_id":"22959","supplementarymaterial":"no","OA_place":"publisher","acknowledgement":"Research in the lab of H.A. is supported by the National Institutes of Health (R01EB033172, R01EB035430, and R01AG077773).\r\n\r\nResearch in the lab of F.H.A. is supported by the US Army Research Office cooperative agreement for the Institute for Collaborative Biotechnologies (W911NF-19-2-0026) and the US Department of Energy, Office of Science, Office of Basic Energy Sciences (DE-SC0021141). This report was prepared as an account of work sponsored by an agency of the US Government. Neither the US Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the US Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the US Government or any agency thereof.\r\n\r\nResearch in the lab of D.B. has been supported by National Institutes of Health (NIH) (R35-GM158123-01 and R01-GM068462).\r\n\r\nResearch in the lab of H.B. is supported by grants from the Bill & Melinda Gates Foundation and Oxford Nanopore Technologies.\r\n\r\nResearch in the lab of R.E.C. is supported by grants from the Japan Society for the Promotion of Science (JSPS) (23K26794, 24H00489, and 24H02267), Japan Science and Technology Agency (JST) (JPMJCR25T3), the Mitsubishi Foundation, and the NIH (U01NS123658).\r\n\r\nResearch in the lab of P.C. is supported by grants from the Vidyasirimedhi Institute of Science and Technology (VISTEC), NSRF via the Program Management Unit for Human Resources & Institutional Development (PMU-B) Research and Innovation grant number B05F640089, and KasikornBank Public Company Limited.\r\n\r\nResearch in the lab of R.A.C. is supported by grants from the Natural Sciences and Engineering Research Council of Canada (RGPIN-2021-03484, RGPAS-2021-00017, and ALLRP-597074-24), the Human Frontier Science Program (RGP0004/2022) and the Canada Foundation for Innovation (26503 and 42695). B.J.S. was supported by an NSERC Canada Graduate Research Scholarship.\r\n\r\nResearch in the lab of V.G.H.E. is supported by grants from the European Research Council, ERC (grant number 856446, CUBE), the Novo Nordisk Foundation (Emerging Investigator grant to A.V.; grant number 0061165) and the Research Council of Norway (grant numbers 309558, Centre for Industrial Biotechnology, SFI-IB, and 257622, Bio4Fuels).\r\n\r\nThis project in the lab of R.F. was supported by Robert A. Welch Foundation (AT-0051-20221212), and the Cancer Prevention and Research Institute of Texas (grant RR230018).\r\n\r\nResearch in the lab of M.S.F. is supported by ETH Zurich and the Swiss National Science Foundation (SNSF) under grant number CR00I5-235927.\r\n\r\nThis project in the lab of J.J.G is supported by the NIH (R35 GM141881) and a National Science Foundation (NSF) Graduate Research Fellowship Program to M.C.\r\n\r\nRelated research in the lab of B.H. is supported by the German Research Foundation (DFG) Project Number 391977956—SFB 1357 Microplastics, subproject C03 and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 951375 (ERC Synergy—ArtMotor).\r\n\r\nRelated work in the lab of S.C.L.K. is supported by the NSF under Grant No. 2414074. S.C.L.K. is the Georgia Research Alliance—Vasser Wooley Chair of Molecular Design at Georgia Tech.\r\n\r\nResearch in the lab of N.K. is supported by grants from the JSPS (24H02261).\r\n\r\nThis project in the lab of B.K. was supported by the NIH (R35 GM131923).\r\n\r\nResearch in the lab of R.E.K. on bispecific antibodies is supported by a grant from the Baden-Württemberg Stiftung and various industry collaborations. Past research was funded by the Deutsche Krebshilfe, the BMBF, and the Deutsche Forschungsgemeinschaft.\r\n\r\nResearch in the lab of R.D.L. (Protein Engineering and Structural Genomics group) is supported by grants from Brazilian National Research Council—CNPq (303833/2022-0, 307370/2025-9), the Oswaldo Cruz Fondation—Fiocruz (VPPIS-004-FIO-22, IAM-005-FIO-22, VPPCB-002-FIO25), and the Brazilian National Supercomputing Center—LNCC.\r\n\r\nChemical protein synthesis research in the lab of L.L. is supported by NSFC (22137005, 22227810, T2488301) and New Cornerstone Science Foundation.\r\n\r\nResearch in the lab of M.M.M. is supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (202250/Z/16/Z); the Biotechnology and Biological Sciences Research Council (BB/W015730/1) and a UKRI Postdoc Guarantee Fellowship (Horizon Europe Guarantee via EPSRC EP/Z000823/1 to L.F.G).\r\n\r\nResearch in the lab of F.Z. is partially supported by the Natural Science Foundation of Shaanxi Province (2025SF-YBXM-421).\r\n\r\nResearch in the lab of J.K.N. is supported by the NIH (R35GM155044), Biohub, San Francisco, the Pew Charitable Trusts, The Vallee Foundation, The Shurl and Kay Curci Foundation, the Bakar Fellows Program, and a Sloan Research Fellowship. I.J.O. acknowledges support from a Gilliam Fellowship from the Howard Hughes Medical Institute.\r\n\r\nResearch in the lab of J.N.P. is supported by the Natural Science and Engineering Research Council of Canada (RGPIN-N-2018-04686) and the Canada Research Chair in Engineering of Applied Proteins (CRC-2020-00171). D.J.F. is supported by a fellowship from the Fonds de recherche du Québec.\r\n\r\nResearch in the lab of A.P. has been supported predominantly by grants from the SNSF, the European Union, the European Research Council, as well as by pre- and postdoctoral fellowships to the co-workers.\r\n\r\nResearch in the lab of Y.Q. is supported by a Horizon Europe Guarantee ERC Starting Grant (EP/Z000351/1) and a Biotechnology and Biological Sciences Research Council Research Grant (BB/W00349X/1).\r\n\r\nJ.C.R. acknowledges partial support from the SNSF Postdoc.Mobility (P500PN_214290). The author thanks Chenghao Liu and Jason Yang for fruitful discussions.\r\n\r\nResearch in the lab of S.S. is supported by a NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO, VI.Vidi.213.025) and the European Research Council, ERC (grant agreement number 101075934, ReCNNSTRCT).\r\n\r\nResearch in the lab of J.B.S. is supported by a Helmsley Charitable Trust grant and a Swim Across America grant.\r\n\r\nThis project in the lab of C.L.T. was supported by a grant from the National Institute of General Medical Sciences of the NIH (R35GM136367).\r\n\r\nResearch on ncAAs in the lab of J.A.V. is supported by a grant from the National Institute of General Medical Sciences of the NIH (R35GM133471) and a grant from the NSF (2339201). The content is solely the responsibility of the author and does not necessarily represent the official views of the NIH or the NSF.\r\n\r\nResearch in the lab of A.M.W is supported by an NIH Director’s New Innovator Award (DP2GM149548), a David and Lucille Packard Fellowship for Science and Engineering (2021-73007), an Ono Pharma Foundation Breakthrough Science Initiative Award (149802896), and the University of Wisconsin—Madison Department of Biochemistry.\r\n\r\nProjects in the lab of A.H-W.Y. are supported by NIH/NIBIB R00EB031913, UCSC startup/Innovation Catalyst Grant, and Chan Zuckerberg Initiative (2024-337820).\r\n\r\nResearch in the lab of J.Zhang is supported by NIH grants R35 CA197622, R01 DK073368, R01 DE030497, R01 HL162302, R01 CA262815, and RF1 MH126707.\r\n\r\nResearch in the lab of H. Z. is supported by the DOE Center for Advanced Bioenergy and Bioproducts Innovation (U.S. Department of Energy, Office of Science, Biological and Environmental Research Program under Award Number DE-SC0018420), National Science Foundation (NSF) (DBI-2400058, OISE-2435374, IIS-2435755, and CHE-2505932), and National Institutes of Health (NIH) (AI144967). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the DOE, NSF or NIH.\r\n\r\nThe authors are grateful to the anonymous peer reviewers and to Anna Devor for inspiration and guidance for preparing this manuscript.","title":"Protein engineering: Status report","status":"public","dataavailabilitystatement":"No new data were generated or analysed in support of this research.","abstract":[{"lang":"eng","text":"With this status report, we aim to provide a timely snapshot of the protein engineering field as a broad and rapidly advancing discipline that integrates computational, molecular biology, structure-guided, evolutionary, and synthetic approaches to create new and improved proteins with tailored structures and useful functions. The report is organized into eight thematic areas spanning core methodologies and major application domains, including enzymes, therapeutics, detection, synthetic biology, and materials. Contributions from experts across these areas highlight both the historical foundations and recent advances in their respective fields, with particular emphasis on the growing influence of machine learning and artificial intelligence-based methods. Emerging from this broad overview is a central message: protein engineering appears to be entering a golden age, defined by a rapidly accelerating pace of progress, even as significant challenges in design, screening, and real-world application remain. Looking ahead, the continued integration of computational and experimental strategies is poised to further accelerate the impact of protein engineering across an expanding range of economically and societally important sectors, from therapeutics and molecular imaging to diagnostics, plastic recycling, and industrial chemistry."}],"year":"2026","month":"07","type":"journal_article","publication_identifier":{"eissn":["1741-0134"],"issn":["1741-0126"]},"researchdata_availability":"no","external_id":{"pmid":["42466865"]},"doi":"10.1093/protein/gzag020","date_published":"2026-07-17T00:00:00Z"},{"title":"Data heterogeneity and personalization in federated learning","status":"public","corr_author":"1","year":"2026","abstract":[{"lang":"eng","text":"In recent years there has been a massive increase in the amount of data generated in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones, have become\r\nubiquitous in most societies on earth. Through text typed, photos taken and apps used,\r\nthese devices, which we refer to as clients, generate enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of these devices means the data they generate is often\r\nsensitive and privacy concerns prevent it being gathered and stored in a central location. This\r\npresents a challenge to the modern machine learning paradigm that requires central access\r\nto large amounts of data. Federated learning (FL) has emerged as one of the answers to\r\nthis problem. Rather than bringing the data to the model, FL sends the model to the data.\r\nModel training takes place on device, with periodically synchronized updates, allowing data to\r\nremain locally stored. While this approach offers significant privacy advantages it comes with\r\nits own set of unique challenges. These include: data heterogeneity, the notion that different\r\ndevices generate data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity, meaning that different devices may have differing hardware specifications; high\r\ncommunication costs, which are induced by the repeated transferring of models over the\r\nnetwork and low device computational power, which limits the use of larger models on device.\r\nIn this thesis we present a range of methods for federated learning. We focus primarily on\r\nthe challenge of data heterogeneity, though the methods presented are designed to be well\r\nadapted to the other challenges of a federated setting, such as the constraints of limited\r\ncompute and communication overhead. We first present a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates clients as samples from a certain probability\r\ndistribution and infers the parameters of this distribution from the available training clients.\r\nThis learned distribution then represents the heterogeneity present among the clients and can\r\nbe sampled from in order to create new simulated clients that are similar to the real clients we\r\nhave observed so far. Following this we present two methods for directly dealing with data\r\nheterogeneity through personalization. Highly heterogeneous client data distributions can mean\r\nthat learning a single global model becomes suboptimal, and some form of personalization of\r\nmodels to each individual client is required. Our approaches are based around hypernetworks,\r\nwhich we use to generate personalized model parameters without the need for additional\r\ntraining or finetuning. In the first approach we focus on generating full parameterizations of\r\nclient models using learned embeddings of client data and labels, with a hypernetwork located\r\non the central server. In the second approach we address the more challenging scenario where\r\nwe want to generate a personalized model for a client without any label information. The\r\nhypernetwork is trained to generate a low dimensional representation of a client’s personalized\r\nmodel parameters, allowing it to be transferred to and run on the client devices. In our final\r\npresented method, we change our focus and rather than aim to directly address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected by it. This is done in the context\r\nof k-means clustering and we present a method for federated clustering with a focus on added\r\nprivacy guarantees."}],"acknowledgement":"This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12]. Furthermore, the candidate acknowledges the support from the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","OA_place":"publisher","day":"09","alternative_title":["ISTA Thesis"],"citation":{"apa":"Scott, J. A. (2026). <i>Data heterogeneity and personalization in federated learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21198\">https://doi.org/10.15479/AT-ISTA-21198</a>","ama":"Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21198\">10.15479/AT-ISTA-21198</a>","ieee":"J. A. Scott, “Data heterogeneity and personalization in federated learning,” Institute of Science and Technology Austria, 2026.","ista":"Scott JA. 2026. Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria.","short":"J.A. Scott, Data Heterogeneity and Personalization in Federated Learning, Institute of Science and Technology Austria, 2026.","chicago":"Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated Learning.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21198\">https://doi.org/10.15479/AT-ISTA-21198</a>.","mla":"Scott, Jonathan A. <i>Data Heterogeneity and Personalization in Federated Learning</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21198\">10.15479/AT-ISTA-21198</a>."},"_id":"21198","file":[{"file_size":272379252,"date_updated":"2026-02-17T11:46:22Z","content_type":"application/zip","creator":"jscott","access_level":"closed","date_created":"2026-02-17T11:46:22Z","relation":"source_file","checksum":"121c1d968bd86f3630aa7e81d5bbbcb0","file_name":"2026_Scott_Jonathan_Thesis_Source.zip","file_id":"21298"},{"content_type":"application/pdf","creator":"jscott","access_level":"open_access","date_created":"2026-02-27T10:25:41Z","file_size":15220298,"date_updated":"2026-02-27T10:25:41Z","file_name":"2026_Jonathan_Scott_Thesis.pdf","success":1,"file_id":"21366","relation":"main_file","checksum":"6e3e08ba474bbee8511cc8a839ab2077"}],"has_accepted_license":"1","publication_status":"published","doi_confirm":"1","doi":"10.15479/AT-ISTA-21198","date_published":"2026-02-09T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"page":"158","type":"dissertation","month":"02","date_created":"2026-02-09T14:59:53Z","degree_awarded":"PhD","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-01T09:29:03Z","related_material":{"record":[{"status":"public","id":"21207","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"20819","status":"public"},{"relation":"part_of_dissertation","id":"17411","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18120"}]},"file_date_updated":"2026-02-27T10:25:41Z","ddc":["005"],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","author":[{"full_name":"Scott, Jonathan A","last_name":"Scott","first_name":"Jonathan A","id":"e499926b-f6e0-11ea-865d-9c63db0031e8"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-21198","project":[{"name":"Bilateral Artificial Intelligence (Lampert)","_id":"d8f03aaa-b035-11f1-8588-d5147fa879e0","grant_number":"COE12"}],"language":[{"iso":"eng"}]},{"file_date_updated":"2026-05-13T13:10:48Z","ddc":["000"],"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","date_created":"2026-05-11T08:43:22Z","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-10-01T09:32:47Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"14771","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"21858"},{"id":"21859","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"21857","status":"public"},{"status":"public","id":"18121","relation":"part_of_dissertation"}]},"project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-21854","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"author":[{"orcid":"0000-0002-7778-3221","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","first_name":"Eugenia B","last_name":"Iofinova","full_name":"Iofinova, Eugenia B"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"supervisor":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"alternative_title":["ISTA Thesis"],"day":"11","citation":{"ama":"Iofinova EB. On the utility and effects of efficiency in artificial neural networks. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21854\">10.15479/AT-ISTA-21854</a>","ieee":"E. B. Iofinova, “On the utility and effects of efficiency in artificial neural networks,” Institute of Science and Technology Austria, 2026.","apa":"Iofinova, E. B. (2026). <i>On the utility and effects of efficiency in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21854\">https://doi.org/10.15479/AT-ISTA-21854</a>","chicago":"Iofinova, Eugenia B. “On the Utility and Effects of Efficiency in Artificial Neural Networks.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21854\">https://doi.org/10.15479/AT-ISTA-21854</a>.","mla":"Iofinova, Eugenia B. <i>On the Utility and Effects of Efficiency in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21854\">10.15479/AT-ISTA-21854</a>.","ista":"Iofinova EB. 2026. On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria.","short":"E.B. Iofinova, On the Utility and Effects of Efficiency in Artificial Neural Networks, Institute of Science and Technology Austria, 2026."},"das_tickbox":"1","_id":"21854","file":[{"creator":"eiofinov","content_type":"application/zip","access_level":"closed","date_created":"2026-05-11T08:36:01Z","file_size":28479571,"date_updated":"2026-05-11T08:36:01Z","file_name":"EIofinova_thesis_FinalVersion.zip","file_id":"21856","relation":"source_file","checksum":"2e148dad920e3f9b7c32796e0ba2e5f7"},{"date_updated":"2026-05-13T13:10:48Z","file_size":18137757,"content_type":"application/pdf","creator":"eiofinov","date_created":"2026-05-13T13:10:48Z","access_level":"open_access","checksum":"b10c2933f386f532b2dbf28b19c5525c","relation":"main_file","file_name":"2026_Iofinova_Eugenia_Thesis.pdf","file_id":"21877","success":1}],"has_accepted_license":"1","publication_status":"published","status":"public","title":"On the utility and effects of efficiency in artificial neural networks","corr_author":"1","abstract":[{"text":"As neural-network-based models grow both in size and popularity, interest has grown in making the models smaller and more efficient to train. To that end, many methods have been proposed to prune models by reducing their number of nonzero parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller number of parameters than the total contained in the model is updated during training, has become very popular, especially in the space of Large Language Models. At the same time, the increasingly routine deployment of machine learning in real-world applications has spurred a drive to make them more trustworthy - in the sense of, among other things, being unbiased, interpretable, and editable. In this thesis, we examine the interplay between efficiency and trustworthiness.\r\n\r\nFirst, we analyze the effects of model pruning on bias in computer vision models, demonstrating that increased sparsity leads to greater bias, largely as a function of increased model uncertainty in marginal cases. Based on this observation, we propose several bias mitigation techniques. Then, we demonstrate that example-specific model pruning can improve model interpretation methods while improving pruning efficiency to make example-specific model pruning feasible in real time. Then, we investigate the effectiveness of parameter-efficient and data-efficient model personalization via fine-tuning, demonstrating that it is highly feasible with very small computational and data resources. Finally, we consider efficiency in editing model knowledge using a custom synthetic data framework, demonstrating that parameter-efficient, low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally, that restricting which model blocks are fine-tuned frequently improves results. Together, the results in this thesis provide new insights and techniques for combining trustworthiness and efficiency during neural network inference and training.\r\n\r\n","lang":"eng"}],"year":"2026","publisher_comment":"In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of ISTA's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.","OA_place":"publisher","acknowledgement":"The research in this Ph.D. was funded in whole\r\nor in part by the Austrian Science Fund (FWF) W1260-N35 (Vienna Graduate School for\r\nComputational Optimization). For open access purposes the author has applied a CC BY\r\npublic copyright license to any author accepted manuscript version arising from this submission\r\nwherever possible. Additionally, I am grateful to Alois Schlögl, Waleed Khalid, and the rest of\r\nthe ISTA Scientific Computing team for building and maintaining the infrastructure I used\r\nto run experiments. I’m also deeply grateful to the Alistarh group’s administrative assistant,\r\nChristine Francois, who always deals with our nonsense with common sense and a smile.\r\n","page":"237","type":"dissertation","month":"05","doi_confirm":"1","date_published":"2026-05-11T00:00:00Z","doi":"10.15479/AT-ISTA-21854","publication_identifier":{"issn":["2663-337X"]}},{"fulldoi":"https://doi.org/10.1093/mnras/stag1567","intvolume":"       551","issue":"3","language":[{"iso":"eng"}],"OA_type":"gold","department":[{"_id":"JoMa"}],"article_processing_charge":"Yes","author":[{"last_name":"de Graaff","full_name":"de Graaff, Anna","first_name":"Anna"},{"first_name":"Raphael E","full_name":"Hviding, Raphael E","last_name":"Hviding"},{"first_name":"Rohan P","last_name":"Naidu","full_name":"Naidu, Rohan P"},{"full_name":"Greene, Jenny E","last_name":"Greene","first_name":"Jenny E"},{"last_name":"Miller","full_name":"Miller, Tim B","first_name":"Tim B"},{"full_name":"Leja, Joel","last_name":"Leja","first_name":"Joel"},{"full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"full_name":"Katz, Harley","last_name":"Katz","first_name":"Harley"},{"full_name":"Bezanson, Rachel","last_name":"Bezanson","first_name":"Rachel"},{"first_name":"Leindert A","last_name":"Boogaard","full_name":"Boogaard, Leindert A"},{"last_name":"Bose","full_name":"Bose, Sownak","first_name":"Sownak"},{"first_name":"John","full_name":"Chisholm, John","last_name":"Chisholm"},{"first_name":"Nikko J","last_name":"Cleri","full_name":"Cleri, Nikko J"},{"first_name":"Pratika","full_name":"Dayal, Pratika","last_name":"Dayal"},{"full_name":"Feldmann, Robert","last_name":"Feldmann","first_name":"Robert"},{"last_name":"Fudamoto","full_name":"Fudamoto, Yoshinobu","first_name":"Yoshinobu"},{"full_name":"Fujimoto, Seiji","last_name":"Fujimoto","first_name":"Seiji"},{"full_name":"Furtak, Lukas J","last_name":"Furtak","first_name":"Lukas J"},{"full_name":"Glazebrook, Karl","last_name":"Glazebrook","first_name":"Karl"},{"first_name":"Rashmi","last_name":"Gottumukkala","full_name":"Gottumukkala, Rashmi"},{"first_name":"Kasper E","last_name":"Heintz","full_name":"Heintz, Kasper E"},{"first_name":"Vasily","last_name":"Kokorev","full_name":"Kokorev, Vasily"},{"full_name":"Labbe, Ivo","last_name":"Labbe","first_name":"Ivo"},{"first_name":"Michael V","last_name":"Maseda","full_name":"Maseda, Michael V"},{"first_name":"Ian","last_name":"McConachie","full_name":"McConachie, Ian"},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"first_name":"Erica","full_name":"Nelson, Erica","last_name":"Nelson"},{"first_name":"Przemysław","full_name":"Nowaczyk, Przemysław","last_name":"Nowaczyk"},{"first_name":"Pascal A","last_name":"Oesch","full_name":"Oesch, Pascal A"},{"last_name":"Rix","full_name":"Rix, Hans-Walter","first_name":"Hans-Walter"},{"last_name":"Setton","full_name":"Setton, David J","first_name":"David J"},{"last_name":"Torralba Torregrosa","full_name":"Torralba Torregrosa, Alberto","id":"018f0249-0e87-11f0-b167-cbce08fbd541","first_name":"Alberto","orcid":"0000-0001-5586-6950"},{"last_name":"Walter","full_name":"Walter, Fabian","first_name":"Fabian"},{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"first_name":"Arjen","full_name":"van der Wel, Arjen","last_name":"van der Wel"}],"scopus_import":"1","oa":1,"article_number":"stag1567","volume":551,"ddc":["520"],"file_date_updated":"2026-10-01T11:25:20Z","publisher":"Oxford University Press","oa_version":"Published Version","article_type":"original","date_created":"2026-09-17T11:06:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-01T11:31:16Z","PlanS_conform":"1","type":"journal_article","month":"09","arxiv":1,"doi":"10.1093/mnras/stag1567","date_published":"2026-09-01T00:00:00Z","researchdata_availability":"yes","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"external_id":{"arxiv":["2511.21820"]},"citation":{"ista":"de Graaff A, Hviding RE, Naidu RP, Greene JE, Miller TB, Leja J, Matthee JJ, Brammer G, Katz H, Bezanson R, Boogaard LA, Bose S, Chisholm J, Cleri NJ, Dayal P, Feldmann R, Fudamoto Y, Fujimoto S, Furtak LJ, Glazebrook K, Gottumukkala R, Heintz KE, Kokorev V, Labbe I, Maseda MV, McConachie I, Nanayakkara T, Nelson E, Nowaczyk P, Oesch PA, Rix H-W, Setton DJ, Torralba Torregrosa A, Walter F, Wang B, Weibel A, van der Wel A. 2026. Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy. Monthly Notices of the Royal Astronomical Society. 551(3), stag1567.","short":"A. de Graaff, R.E. Hviding, R.P. Naidu, J.E. Greene, T.B. Miller, J. Leja, J.J. Matthee, G. Brammer, H. Katz, R. Bezanson, L.A. Boogaard, S. Bose, J. Chisholm, N.J. Cleri, P. Dayal, R. Feldmann, Y. Fudamoto, S. Fujimoto, L.J. Furtak, K. Glazebrook, R. Gottumukkala, K.E. Heintz, V. Kokorev, I. Labbe, M.V. Maseda, I. McConachie, T. Nanayakkara, E. Nelson, P. Nowaczyk, P.A. Oesch, H.-W. Rix, D.J. Setton, A. Torralba Torregrosa, F. Walter, B. Wang, A. Weibel, A. van der Wel, Monthly Notices of the Royal Astronomical Society 551 (2026).","chicago":"de Graaff, Anna, Raphael E Hviding, Rohan P Naidu, Jenny E Greene, Tim B Miller, Joel Leja, Jorryt J Matthee, et al. “Little Red Dots Host Black Hole Stars: A Unified Family of Gas-Reddened AGN Revealed by JWST/NIRSpec Spectroscopy.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/mnras/stag1567\">https://doi.org/10.1093/mnras/stag1567</a>.","mla":"de Graaff, Anna, et al. “Little Red Dots Host Black Hole Stars: A Unified Family of Gas-Reddened AGN Revealed by JWST/NIRSpec Spectroscopy.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 551, no. 3, stag1567, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/mnras/stag1567\">10.1093/mnras/stag1567</a>.","apa":"de Graaff, A., Hviding, R. E., Naidu, R. P., Greene, J. E., Miller, T. B., Leja, J., … van der Wel, A. (2026). Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stag1567\">https://doi.org/10.1093/mnras/stag1567</a>","ama":"de Graaff A, Hviding RE, Naidu RP, et al. Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy. <i>Monthly Notices of the Royal Astronomical Society</i>. 2026;551(3). doi:<a href=\"https://doi.org/10.1093/mnras/stag1567\">10.1093/mnras/stag1567</a>","ieee":"A. de Graaff <i>et al.</i>, “Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 551, no. 3. Oxford University Press, 2026."},"day":"01","das_tickbox":"1","quality_controlled":"1","publication":"Monthly Notices of the Royal Astronomical Society","_id":"22960","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"file_id":"23026","file_name":"2026_MonthNoticesRAS_deGraaff.pdf","relation":"main_file","checksum":"a82b93954671a12bb60d8d7a4a4d526b","access_level":"open_access","date_created":"2026-10-01T11:25:20Z","creator":"dernst","content_type":"application/pdf","file_size":14983705,"date_updated":"2026-10-01T11:25:20Z"}],"publication_status":"published","has_accepted_license":"1","title":"Little red dots host black hole stars: A unified family of gas-reddened AGN revealed by JWST/NIRSpec spectroscopy","status":"public","dataavailabilitystatement":"All data used in this work are publicly available through the\r\nDAWN JWST Archive (https://dawn-cph.github.io/dja/index.h\r\ntml). The spectra used in this work are part of version 4.5 of the\r\nDJA (G. Brammer & F. Valentino 2025). We also release our complete LRD catalogue, together with all key measurements made All data used in this work are publicly available through the\r\nDAWN JWST Archive (https://dawn-cph.github.io/dja/index.h\r\ntml). The spectra used in this work are part of version 4.5 of the\r\nDJA (G. Brammer & F. Valentino 2025). We also release our complete LRD catalogue, together with all key measurements made in the modified blackbody fitting and emission-line fitting. The\r\ntable can be found at https://doi.org/10.5281/zenodo.21977747,\r\nand its contents are described in Appendix B.\r\n\r\n","abstract":[{"lang":"eng","text":"We construct and characterize a sample of 146 little red dots (LRDs) across 2.0<z<9.3, selecting all sources with v-shaped\r\nultraviolet (UV)–optical continua from James Webb Space Telescope (JWST) NIRSpec/PRISM spectra and compact morphologies in NIRCam/F444W imaging. We show that LRD continuum spectra are well described by modified blackbodies\r\nacross ∼ 0.4 − 1.0 µm, with typical T ∼ 5000 K (λpeak ∼ 0.65 µm) across 2 dex in luminosity, and a tail toward T ∼ 2000 K.\r\nLRDs therefore trace a locus in the Hertzsprung–Russell diagram that is analogous to stars on the Hayashi track, strongly\r\nsupporting the picture that LRDs are active galactic nucleus (AGN) embedded in optically thick dense gas envelopes.\r\nHotter LRDs with λpeak < 0.65 µm typically have strong Balmer breaks, redder UV slopes, and high optical luminosities;\r\nother LRDs show weak or no Balmer breaks, and wide variety in βUV and L5100. Crucially, we demonstrate that the UV–\r\noptical continua are strongly linked to the Hα, Hβ, [O iii], and O i line properties. There is a tight linear relation between\r\nthe Hα and optical continuum luminosities, as well as Hα and O i λ8446, indicating that Balmer, O i, and optical emission\r\nmust primarily be powered by the same source. The Balmer decrement increases strongly toward higher LHα, L5100, and\r\nBalmer break strength, providing key evidence for luminosity-dependent effects of collisional (de-)excitation and resonant\r\nscattering in the gaseous envelopes. In contrast, we show that [O iii] emission likely originates from star-forming host\r\ngalaxies, with strong variation in the AGN-to-host ratio among the LRD population. Our work presents an empirical\r\ndescription of the nature and structure of LRDs, defining a new benchmark for ongoing LRD model developments."}],"year":"2026","supplementarymaterial":"yes","DOAJ_listed":"1","OA_place":"publisher","acknowledgement":"AdG thanks Devesh Nandal for discussions on the properties\r\nof convective envelopes and Hayashi limit, and the students of\r\nthe I-HOW JWST Workshop (Barbora Adamcova, Biswaraj Palit,\r\nOlena Pastoven, and Weronika Puchalska) for their help in producing an early version of Figs 8 and 10. This work is based on\r\nobservations made with the NASA/ESA/CSA James Webb Space\r\nTelescope. The data were obtained from the Mikulski Archive for\r\nSpace Telescopes at the Space Telescope Science Institute, which\r\nis operated by the Association of Universities for Research in\r\nAstronomy, Inc., under NASA contract NAS 5-03127 for JWST.\r\nThese observations are associated with programs 1180, 1181,\r\n1208, 1212, 1213, 1215, 1286, 1345, 1433, 2198, 2561, 2750, 2767,\r\n4106, 4233, 5105, 5224, 6368, and 6585. Support for program no.\r\n4233 was provided by NASA through a grant from the Space\r\nTelescope Science Institute, which is operated by the Association\r\nof Universities for Research in Astronomy, Inc., under NASA\r\ncontract NAS 5-03127.\r\nAdG acknowledges support from a Clay Fellowship awarded by\r\nthe Smithsonian Astrophysical Observatory. REH acknowledges\r\nsupport by the German Aerospace Center (DLR) and the Federal\r\nMinistry for Economic Affairs and Energy (BMWi) through program 50OR2403 ‘RUBIES’. The Cosmic Dawn Centerisfunded by\r\nthe Danish National Research Foundation (DNRF) under grant\r\nno. 140. This work has received funding from the Swiss State\r\nSecretariat for Education, Research and Innovation (SERI) under\r\ncontract no. MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349.\r\nTBM was supported by a CIERA fellowship. PD warmly acknowledges support from an NSERC discovery grant (RGPIN-2025-\r\n06182). KG acknowledges support from Australian Research\r\nCouncil Laureate Fellowship FL180100060. LAB acknowledges\r\nsupport from the Dutch Research Council (NWO) under grant\r\nVI.Veni.242.055 (https://doi.org/10.61686/LAJVP77714) and the\r\nERC Consolidator grant 101088676 (‘VOYAJ’). YF is supported by\r\nJSPS KAKENHI grant nos JP22K21349 and JP23K13149."},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","checksum":"902cc8d177c8d3ae9cfe07c30375c9a9","file_name":"2026_PhysicalReviewE_DiazMelian.pdf","success":1,"file_id":"22014","file_size":3173197,"date_updated":"2026-06-16T11:21:53Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2026-06-16T11:21:53Z"}],"has_accepted_license":"1","publication_status":"published","day":"14","citation":{"chicago":"Diaz Melian, Vicente L, Isaac C Lenton, Jack Binysh, Anton Souslov, and Scott R Waitukaitis. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” <i>Physical Review E</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/m7gr-2t6j\">https://doi.org/10.1103/m7gr-2t6j</a>.","mla":"Diaz Melian, Vicente L., et al. “Geometry of the Vapor Layer under a Leidenfrost Hydrogel Sphere.” <i>Physical Review E</i>, vol. 113, no. 5, L053502, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/m7gr-2t6j\">10.1103/m7gr-2t6j</a>.","ista":"Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. 2026. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. Physical Review E. 113(5), L053502.","short":"V.L. Diaz Melian, I.C. Lenton, J. Binysh, A. Souslov, S.R. Waitukaitis, Physical Review E 113 (2026).","ieee":"V. L. Diaz Melian, I. C. Lenton, J. Binysh, A. Souslov, and S. R. Waitukaitis, “Geometry of the vapor layer under a Leidenfrost hydrogel sphere,” <i>Physical Review E</i>, vol. 113, no. 5. American Physical Society, 2026.","ama":"Diaz Melian VL, Lenton IC, Binysh J, Souslov A, Waitukaitis SR. Geometry of the vapor layer under a Leidenfrost hydrogel sphere. <i>Physical Review E</i>. 2026;113(5). doi:<a href=\"https://doi.org/10.1103/m7gr-2t6j\">10.1103/m7gr-2t6j</a>","apa":"Diaz Melian, V. L., Lenton, I. C., Binysh, J., Souslov, A., &#38; Waitukaitis, S. R. (2026). Geometry of the vapor layer under a Leidenfrost hydrogel sphere. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/m7gr-2t6j\">https://doi.org/10.1103/m7gr-2t6j</a>"},"quality_controlled":"1","publication":"Physical Review E","_id":"21982","acknowledgement":"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 Shop and the Scientific Computing Facility. J.B. acknowledges funding from the European Union's Horizon research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101106500.","OA_place":"publisher","status":"public","title":"Geometry of the vapor layer under a Leidenfrost hydrogel sphere","corr_author":"1","abstract":[{"lang":"eng","text":"A floating Leidenfrost droplet exhibits curvature inversion of its underside, due to the balance of vapor pressure and surface tension. Using interferometric imaging, we find different behavior for a levitated hydrogel sphere. Curvature inversion is observed briefly just after deposition, but quickly gives way to a steady state with no inversion. We show the essential role of vaporization in shaping the underbelly of the hydrogel, where changes due to direct mass loss are more significant than the balance of vapor pressure and elastic forces."}],"year":"2026","month":"05","type":"journal_article","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"external_id":{"arxiv":["2507.04982"]},"arxiv":1,"doi":"10.1103/m7gr-2t6j","date_published":"2026-05-14T00:00:00Z","publisher":"American Physical Society","oa_version":"Published Version","article_type":"letter_note","volume":113,"ddc":["530"],"file_date_updated":"2026-06-16T11:21:53Z","date_updated":"2026-10-02T08:44:47Z","PlanS_conform":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"23005"}]},"date_created":"2026-06-10T07:36:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/m7gr-2t6j","issue":"5","intvolume":"       113","article_number":"L053502","author":[{"last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L"},{"last_name":"Lenton","full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C"},{"first_name":"Jack","full_name":"Binysh, Jack","last_name":"Binysh"},{"full_name":"Souslov, Anton","last_name":"Souslov","first_name":"Anton"},{"full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}],"department":[{"_id":"ScWa"},{"_id":"GradSch"}],"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"oa":1,"scopus_import":"1"},{"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-23005","supervisor":[{"first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis"}],"article_processing_charge":"No","author":[{"last_name":"Diaz Melian","full_name":"Diaz Melian, Vicente L","id":"b6798902-eea0-11ea-9cbc-a8e14286c631","first_name":"Vicente L"}],"department":[{"_id":"GradSch"},{"_id":"ScWa"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","file_date_updated":"2026-09-29T09:56:46Z","ddc":["530","530","530"],"date_updated":"2026-10-02T08:44:47Z","related_material":{"record":[{"status":"public","id":"14514","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"21982","status":"public"}]},"date_created":"2026-09-28T17:40:23Z","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"09","page":"114","type":"dissertation","researchdata_availability":"yes","publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","doi":"10.15479/AT-ISTA-23005","date_published":"2026-09-29T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2026_diaz-melian_vicente_Thesis.pdf","file_id":"23007","checksum":"f339bdee0a6925573687de928ca525dc","relation":"main_file","creator":"vdiazmel","content_type":"application/pdf","date_created":"2026-09-29T09:22:27Z","access_level":"open_access","date_updated":"2026-09-29T09:56:46Z","file_size":8463804},{"access_level":"closed","date_created":"2026-09-29T09:49:32Z","content_type":"application/zip","creator":"vdiazmel","file_size":4028974886,"date_updated":"2026-09-29T09:56:46Z","file_id":"23008","file_name":"2026_diaz-melian_vicente_Thesis.zip","relation":"source_file","checksum":"5b17122895fc419bfb620e23bfe7780a"}],"has_accepted_license":"1","publication_status":"published","day":"29","citation":{"ama":"Diaz Melian VL. The morphology underneath a levitated hydrogel sphere. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23005\">10.15479/AT-ISTA-23005</a>","ieee":"V. L. Diaz Melian, “The morphology underneath a levitated hydrogel sphere,” Institute of Science and Technology Austria, 2026.","apa":"Diaz Melian, V. L. (2026). <i>The morphology underneath a levitated hydrogel sphere</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-23005\">https://doi.org/10.15479/AT-ISTA-23005</a>","chicago":"Diaz Melian, Vicente L. “The Morphology underneath a Levitated Hydrogel Sphere.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-23005\">https://doi.org/10.15479/AT-ISTA-23005</a>.","mla":"Diaz Melian, Vicente L. <i>The Morphology underneath a Levitated Hydrogel Sphere</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23005\">10.15479/AT-ISTA-23005</a>.","ista":"Diaz Melian VL. 2026. The morphology underneath a levitated hydrogel sphere. Institute of Science and Technology Austria.","short":"V.L. Diaz Melian, The Morphology underneath a Levitated Hydrogel Sphere, Institute of Science and Technology Austria, 2026."},"alternative_title":["ISTA Thesis"],"_id":"23005","supplementarymaterial":"yes","OA_place":"publisher","title":"The morphology underneath a levitated hydrogel sphere","status":"public","corr_author":"1","year":"2026","abstract":[{"lang":"eng","text":"When a Leidenfrost droplet floats on its own vapor layer, the interplay between vapor pressure, surface tension, and gravity determines its shape, and in the stable regime the underside of the droplet exhibits curvature inversion. Using interferometric imaging, we observe a different behavior for a levitated hydrogel sphere. Curvature inversion appears briefly after deposition, but the continuous vaporization process removes this feature, leading first to an oscillatory regime and eventually to a steady state without curvature inversion. We demonstrate the essential role of vaporization in shaping the hydrogel underbelly, where direct mass loss has a stronger influence than the balance between vapor pressure and elastic forces."}]},{"date_updated":"2026-10-02T10:52:13Z","date_created":"2026-09-23T12:25:43Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","file_date_updated":"2026-10-01T12:34:18Z","ddc":["570","576","579"],"supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"CaGu"}],"author":[{"last_name":"Gruber","full_name":"Gruber, Nathalie","id":"2C9C8316-AA17-11E9-B5C2-8BC2E5697425","first_name":"Nathalie"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15479/AT-ISTA-22981","project":[{"_id":"34cb8730-11ca-11ed-8bc3-8b3b3752a6f6","name":"Uncovering the organisational principle of bacterial genomic islands in Anti-phage defense","grant_number":"26422"}],"OA_place":"publisher","acknowledgement":"I want to acknowledge the Austrian Academy of Sciences for funding through the DOC \r\nFellowship program (fellowship number 26422) and for the honest and inspirational talk by \r\nAnton Zeilinger at the award ceremony about the PhD journey. ","status":"public","title":"Genetic strategies enabling bacterial adaptation to selective pressures","corr_author":"1","year":"2026","file":[{"date_created":"2026-10-01T09:00:53Z","access_level":"closed","creator":"ngruber","content_type":"application/pdf","date_updated":"2026-10-01T12:34:18Z","file_size":48619027,"embargo":"2027-10-01","file_id":"23020","file_name":"2026_Gruber_Nathalie_Thesis.pdf","embargo_to":"open_access","checksum":"64a61a8812cefaaeffc247a409d46a23","relation":"main_file"},{"creator":"ngruber","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2026-10-01T09:31:20Z","access_level":"closed","date_updated":"2026-10-01T11:49:41Z","file_size":55175414,"file_name":"2026_Gruber_Nathalie_Thesis.docx","file_id":"23021","checksum":"942f6291750664d6d1adfb4f8b5a1735","relation":"source_file"}],"has_accepted_license":"1","publication_status":"published","citation":{"mla":"Gruber, Nathalie. <i>Genetic Strategies Enabling Bacterial Adaptation to Selective Pressures</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22981\">10.15479/AT-ISTA-22981</a>.","chicago":"Gruber, Nathalie. “Genetic Strategies Enabling Bacterial Adaptation to Selective Pressures.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22981\">https://doi.org/10.15479/AT-ISTA-22981</a>.","short":"N. Gruber, Genetic Strategies Enabling Bacterial Adaptation to Selective Pressures, Institute of Science and Technology Austria, 2026.","ista":"Gruber N. 2026. Genetic strategies enabling bacterial adaptation to selective pressures. Institute of Science and Technology Austria.","ieee":"N. Gruber, “Genetic strategies enabling bacterial adaptation to selective pressures,” Institute of Science and Technology Austria, 2026.","ama":"Gruber N. Genetic strategies enabling bacterial adaptation to selective pressures. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22981\">10.15479/AT-ISTA-22981</a>","apa":"Gruber, N. (2026). <i>Genetic strategies enabling bacterial adaptation to selective pressures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22981\">https://doi.org/10.15479/AT-ISTA-22981</a>"},"alternative_title":["ISTA Thesis"],"day":"24","_id":"22981","publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","date_published":"2026-09-24T00:00:00Z","doi":"10.15479/AT-ISTA-22981","month":"09","page":"102","type":"dissertation"},{"month":"04","type":"journal_article","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"external_id":{"arxiv":["2407.19908"]},"arxiv":1,"doi":"10.1007/s00332-026-10266-8","date_published":"2026-04-15T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2026_JourNonlinearScience_Bauer.pdf","success":1,"file_id":"21770","relation":"main_file","checksum":"760de2631b6fd7d57bcd5115ed36c0a2","content_type":"application/pdf","creator":"dernst","access_level":"open_access","date_created":"2026-04-28T09:55:32Z","file_size":1108518,"date_updated":"2026-04-28T09:55:32Z"}],"publication_status":"published","has_accepted_license":"1","day":"15","citation":{"chicago":"Bauer, Martin, Sadashige Ishida, and Peter W. Michor. “Symplectic Structures on the Space of Space Curves.” <i>Journal of Nonlinear Science</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00332-026-10266-8\">https://doi.org/10.1007/s00332-026-10266-8</a>.","mla":"Bauer, Martin, et al. “Symplectic Structures on the Space of Space Curves.” <i>Journal of Nonlinear Science</i>, vol. 36, no. 2, 45, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s00332-026-10266-8\">10.1007/s00332-026-10266-8</a>.","short":"M. Bauer, S. Ishida, P.W. Michor, Journal of Nonlinear Science 36 (2026).","ista":"Bauer M, Ishida S, Michor PW. 2026. Symplectic structures on the space of space curves. Journal of Nonlinear Science. 36(2), 45.","ama":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. <i>Journal of Nonlinear Science</i>. 2026;36(2). doi:<a href=\"https://doi.org/10.1007/s00332-026-10266-8\">10.1007/s00332-026-10266-8</a>","ieee":"M. Bauer, S. Ishida, and P. W. Michor, “Symplectic structures on the space of space curves,” <i>Journal of Nonlinear Science</i>, vol. 36, no. 2. Springer Nature, 2026.","apa":"Bauer, M., Ishida, S., &#38; Michor, P. W. (2026). Symplectic structures on the space of space curves. <i>Journal of Nonlinear Science</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00332-026-10266-8\">https://doi.org/10.1007/s00332-026-10266-8</a>"},"publication":"Journal of Nonlinear Science","quality_controlled":"1","_id":"21743","OA_place":"publisher","acknowledgement":"The authors are grateful to Boris Khesin for valuable comments on the MW symplectic structure and S. Ishida thanks Albert Chern for insightful discussions on space curves and Chris Wojtan for his continuous support. M. Bauer was partially supported by NSF grant DMS-1953244 and by the Binational Science Foundation (BSF). S. Ishida was partially supported by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Some figures were generated by the software Houdini and its education license was provided by SideFX. Open access funding provided by University of Vienna.","title":"Symplectic structures on the space of space curves","status":"public","abstract":[{"lang":"eng","text":"We present symplectic structures on the shape space of unparameterized space curves that generalize the classical Marsden–Weinstein structure. Our method integrates the Liouville 1-form of the Marsden–Weinstein structure with Riemannian structures that have been introduced in mathematical shape analysis. We also derive Hamiltonian vector fields for several classical Hamiltonian functions with respect to these new symplectic structures."}],"year":"2026","language":[{"iso":"eng"}],"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"fulldoi":"https://doi.org/10.1007/s00332-026-10266-8","issue":"2","intvolume":"        36","article_number":"45","author":[{"first_name":"Martin","full_name":"Bauer, Martin","last_name":"Bauer"},{"orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","last_name":"Ishida","full_name":"Ishida, Sadashige"},{"first_name":"Peter W.","full_name":"Michor, Peter W.","last_name":"Michor"}],"OA_type":"hybrid","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"article_processing_charge":"Yes (via OA deal)","scopus_import":"1","oa":1,"publisher":"Springer Nature","oa_version":"Published Version","article_type":"original","volume":36,"file_date_updated":"2026-04-28T09:55:32Z","ddc":["510"],"date_updated":"2026-10-02T11:16:45Z","PlanS_conform":"1","related_material":{"record":[{"id":"17361","relation":"earlier_version","status":"public"}]},"date_created":"2026-04-16T07:29:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"author":[{"last_name":"Ishida","full_name":"Ishida, Sadashige","orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige"},{"first_name":"Hugo","last_name":"Lavenant","full_name":"Lavenant, Hugo"}],"OA_type":"hybrid","intvolume":"        26","fulldoi":"https://doi.org/10.1007/s10208-024-09686-3","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-12-21T10:14:37Z","PlanS_conform":"1","date_updated":"2026-10-02T11:17:26Z","ddc":["000"],"file_date_updated":"2026-07-23T05:37:52Z","volume":26,"article_type":"original","oa_version":"Published Version","publisher":"Springer Nature","doi":"10.1007/s10208-024-09686-3","date_published":"2026-02-01T00:00:00Z","arxiv":1,"external_id":{"isi":["001352503300001"],"arxiv":["2312.12213"]},"keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"researchdata_availability":"no","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"type":"journal_article","page":"349-384","month":"02","isi":1,"year":"2026","abstract":[{"text":"We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.","lang":"eng"}],"corr_author":"1","status":"public","title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","OA_place":"publisher","acknowledgement":"The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospitality. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Open access funding provided by Institute of Science and Technology (IST Austria).","supplementarymaterial":"no","_id":"14703","publication":"Foundations of Computational Mathematics","quality_controlled":"1","das_tickbox":"0","day":"01","citation":{"chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” <i>Foundations of Computational Mathematics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s10208-024-09686-3\">https://doi.org/10.1007/s10208-024-09686-3</a>.","mla":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” <i>Foundations of Computational Mathematics</i>, vol. 26, Springer Nature, 2026, pp. 349–84, doi:<a href=\"https://doi.org/10.1007/s10208-024-09686-3\">10.1007/s10208-024-09686-3</a>.","ista":"Ishida S, Lavenant H. 2026. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. 26, 349–384.","short":"S. Ishida, H. Lavenant, Foundations of Computational Mathematics 26 (2026) 349–384.","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. <i>Foundations of Computational Mathematics</i>. 2026;26:349-384. doi:<a href=\"https://doi.org/10.1007/s10208-024-09686-3\">10.1007/s10208-024-09686-3</a>","ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” <i>Foundations of Computational Mathematics</i>, vol. 26. Springer Nature, pp. 349–384, 2026.","apa":"Ishida, S., &#38; Lavenant, H. (2026). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. <i>Foundations of Computational Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10208-024-09686-3\">https://doi.org/10.1007/s10208-024-09686-3</a>"},"publication_status":"published","has_accepted_license":"1","file":[{"date_updated":"2026-07-23T05:37:52Z","file_size":1240012,"date_created":"2026-07-23T05:37:52Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"30671f88e792e8b75ae3e698ac4c131c","relation":"main_file","file_id":"22384","success":1,"file_name":"2026_FoundCompMath_Ishida.pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","department":[{"_id":"HeEd"}],"author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Pach","full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János"}],"oa":1,"scopus_import":"1","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35"},{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"}],"fulldoi":"https://doi.org/10.1007/s00454-025-00796-5","intvolume":"        75","language":[{"iso":"eng"}],"date_created":"2025-11-19T09:44:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-10-02T11:48:00Z","PlanS_conform":"1","related_material":{"record":[{"relation":"earlier_version","id":"17146","status":"public"}]},"volume":75,"ddc":["510"],"file_date_updated":"2026-07-27T08:11:05Z","publisher":"Springer Nature","article_type":"original","oa_version":"Published Version","arxiv":1,"doi":"10.1007/s00454-025-00796-5","date_published":"2026-03-01T00:00:00Z","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"researchdata_availability":"no","external_id":{"isi":["001610592600001"],"arxiv":["2310.14801"]},"page":"597-624","ec_funded":1,"type":"journal_article","month":"03","isi":1,"corr_author":"1","status":"public","title":"Maximum Betti numbers of Čech complexes","abstract":[{"text":"The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². ","lang":"eng"}],"year":"2026","supplementarymaterial":"no","OA_place":"publisher","acknowledgement":"The first author is supported by the European Research Council (ERC), grant no. 788183, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant no. I 02979-N35. The second author is supported by the European Research Council (ERC), grant “GeoScape” and by the Hungarian Science Foundation (NKFIH), grant K-131529. Both authors are supported by the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. Open access funding provided by Institute of Science and Technology (IST Austria).","das_tickbox":"0","quality_controlled":"1","publication":"Discrete & Computational Geometry","citation":{"short":"H. Edelsbrunner, J. Pach, Discrete &#38; Computational Geometry 75 (2026) 597–624.","ista":"Edelsbrunner H, Pach J. 2026. Maximum Betti numbers of Čech complexes. Discrete &#38; Computational Geometry. 75, 597–624.","chicago":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00454-025-00796-5\">https://doi.org/10.1007/s00454-025-00796-5</a>.","mla":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” <i>Discrete &#38; Computational Geometry</i>, vol. 75, Springer Nature, 2026, pp. 597–624, doi:<a href=\"https://doi.org/10.1007/s00454-025-00796-5\">10.1007/s00454-025-00796-5</a>.","apa":"Edelsbrunner, H., &#38; Pach, J. (2026). Maximum Betti numbers of Čech complexes. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00796-5\">https://doi.org/10.1007/s00454-025-00796-5</a>","ama":"Edelsbrunner H, Pach J. Maximum Betti numbers of Čech complexes. <i>Discrete &#38; Computational Geometry</i>. 2026;75:597-624. doi:<a href=\"https://doi.org/10.1007/s00454-025-00796-5\">10.1007/s00454-025-00796-5</a>","ieee":"H. Edelsbrunner and J. Pach, “Maximum Betti numbers of Čech complexes,” <i>Discrete &#38; Computational Geometry</i>, vol. 75. Springer Nature, pp. 597–624, 2026."},"day":"01","_id":"20657","file":[{"date_updated":"2026-07-27T08:11:05Z","file_size":546483,"creator":"dernst","content_type":"application/pdf","date_created":"2026-07-27T08:11:05Z","access_level":"open_access","checksum":"c17c014dbbf5be702195c737890251c8","relation":"main_file","file_name":"2026_DiscreteCompGeom_Edelsbrunner.pdf","file_id":"22410","success":1}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","publication_status":"published"},{"date_published":"2026-03-01T00:00:00Z","doi":"10.3934/fods.2025003","arxiv":1,"keyword":["Topological data analysis","Delaunay mosaic","alpha complex","chromatic sets","persistent homology","kernel/image/cokernel persistent homology","radius function","discrete Morse theory","exact sequences"],"external_id":{"arxiv":["2212.03128"]},"publication_identifier":{"eissn":["2639-8001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.03128"}],"type":"journal_article","ec_funded":1,"page":"30-62","month":"03","year":"2026","abstract":[{"lang":"eng","text":"Motivated by applications in medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided."}],"title":"Chromatic alpha complexes","status":"public","corr_author":"1","OA_place":"repository","acknowledgement":"This project has received funding from the European Research\r\nCouncil (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund\r\n(FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR\r\n109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35.","_id":"20585","citation":{"ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” <i>Foundations of Data Science</i>, vol. 8. AIMS, pp. 30–62, 2026.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. <i>Foundations of Data Science</i>. 2026;8:30-62. doi:<a href=\"https://doi.org/10.3934/fods.2025003\">10.3934/fods.2025003</a>","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian, M. (2026). Chromatic alpha complexes. <i>Foundations of Data Science</i>. AIMS. <a href=\"https://doi.org/10.3934/fods.2025003\">https://doi.org/10.3934/fods.2025003</a>","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” <i>Foundations of Data Science</i>. AIMS, 2026. <a href=\"https://doi.org/10.3934/fods.2025003\">https://doi.org/10.3934/fods.2025003</a>.","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” <i>Foundations of Data Science</i>, vol. 8, AIMS, 2026, pp. 30–62, doi:<a href=\"https://doi.org/10.3934/fods.2025003\">10.3934/fods.2025003</a>.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. 2026. Chromatic alpha complexes. Foundations of Data Science. 8, 30–62.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. 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It lays the foundation for subsequent developmental events, including gastrulation, germ layer specification, organogenesis, and the establishment of the overall body plan. Two major modes of cleavage exist in the animal kingdom: holoblastic (complete) and meroblastic (incomplete) cleavage. Because holoblastic cleavage resembles canonical cytokinesis, its biochemical and mechanical basis has been extensively studied — an annular contractile ring forms at the equator and constricts in a purse-string-like manner, leading to the complete separation of two daughter cells. In contrast, although meroblastic cleavage occurs widely across the animal kingdom (e.g. in fish, reptiles, birds, and cephalopod molluscs), its mechanical basis remains largely unclear. During meroblastic cleavage, the cytokinetic furrow forms only at one pole and does not traverse the entire embryo, raising the question of how cytokinesis proceeds in the absence of a closed contractile ring. Moreover, the resulting daughter cells are not fully separated from the underlying yolk compartment, and how these blastomeres are subsequently cellularised remains unknown. This thesis takes the zebrafish as a model organism to address both questions. The first part characterises the biochemical and mechanical mechanisms underlying non-canonical meroblastic cleavage, revealing a two-phase process in which actomyosin cable contraction and cadherin-mediated membrane adhesion act sequentially to drive furrow ingression and invagination. The second part sheds light on the spatiotemporal dynamics by which individual blastomeres become cellularised, and uncovers a previously unrecognised contribution of central blastomeres to the yolk syncytial layer.","lang":"eng"}],"file":[{"file_name":"2026_TONG_Xin_Thesis.zip","file_id":"22909","relation":"source_file","checksum":"fdcc187a5a92e785da0eff8936fb127e","creator":"xtong","content_type":"application/zip","access_level":"closed","date_created":"2026-09-11T13:04:37Z","file_size":126983933,"date_updated":"2026-09-14T08:28:06Z"},{"date_created":"2026-09-14T12:30:07Z","access_level":"open_access","creator":"xtong","content_type":"application/pdf","date_updated":"2026-09-14T12:48:53Z","file_size":46855054,"file_id":"22930","file_name":"2026_TONG_Xin_Thesis.pdf","checksum":"23ee39b3f08bccd46acfd332e67f5232","relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"has_accepted_license":"1","publication_status":"published","citation":{"apa":"Tong, X. 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Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22777\">10.15479/AT-ISTA-22777</a>.","ista":"Tong X. 2026. Towards a deeper understanding of meroblastic cleavage - supplementary movies, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-22777\">10.15479/AT-ISTA-22777</a>.","short":"X. Tong, (2026)."},"_id":"22777","doi_confirm":"1","date_published":"2026-09-04T00:00:00Z","doi":"10.15479/AT-ISTA-22777","month":"9","ec_funded":1,"type":"research_data"},{"scopus_import":"1","oa":1,"department":[{"_id":"ZoHa"}],"article_processing_charge":"Yes","OA_type":"gold","author":[{"first_name":"Christopher","last_name":"Tiede","full_name":"Tiede, Christopher"},{"id":"3fc12674-2d69-11f1-a6bf-b826b45a1150","first_name":"David W","last_name":"O'Neill","full_name":"O'Neill, David W"},{"first_name":"Daniel J.","last_name":"D’Orazio","full_name":"D’Orazio, Daniel J."}],"article_number":"26","issue":"1","intvolume":"      1008","fulldoi":"https://doi.org/10.3847/1538-4357/ae914e","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-09-20T22:01:48Z","PlanS_conform":"1","date_updated":"2026-10-06T10:45:07Z","ddc":["520"],"file_date_updated":"2026-10-06T10:44:15Z","volume":1008,"article_type":"original","oa_version":"Published Version","publisher":"IOP Publishing","date_published":"2026-09-01T00:00:00Z","doi":"10.3847/1538-4357/ae914e","arxiv":1,"external_id":{"arxiv":["2606.04082"]},"researchdata_availability":"no","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"type":"journal_article","month":"09","abstract":[{"lang":"eng","text":"We investigate whether the nonaccreting phases found in thin, locally isothermal circumbinary disks survive when the disk thermodynamics are evolved self-consistently. We present grid-based hydrodynamics simulations of circumbinary accretion with an energy equation that includes viscous and hydrodynamic heating coupled to radiative blackbody cooling in the high-Mach number regime. We find that, although gas accumulates and heats at the far edge of the circumbinary cavity, the regions that launch accretion streams remain comparatively cold, leading to potentially long-lived suppression of the binary accretion rate as the large-scale feeding rate is reduced towards the Eddington limit. This runaway nonaccretion problem, however, is weakened relative to locally isothermal solutions. Despite their low accretion rates, binaries interacting with disks in a nonaccreting phase can remain sufficiently luminous and variable at optical and near-infrared frequencies to be detectable in upcoming wide-field surveys such as LSST and the Roman Space Telescope. Because of the effective truncation of the surrounding disk, though, such systems are comparatively faint in high energy, photoionizing emission, and may therefore appear as intrinsically X-ray–weak active galactic nuclei with weak or absent emission line features. We additionally suggest an update to grid-based sink prescriptions for approximating mass loss across an unresolved horizon when including an energy conservation equation."}],"year":"2026","status":"public","title":"Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks","OA_place":"publisher","DOAJ_listed":"1","acknowledgement":"This work was supported by the European Union’s Horizon 2023 research and innovation program under Marie Sklodowska-Curie grant agreement No. 101148364, and by Sapere Aude Starting grant No. 121587 through the Danish Independent Research Fund. It was additionally supported by NSF AAG No. 2511544. CT acknowledges many helpful conversations on binary accretion at the workshop Climbing Cosmic Peaks through the Sexten Center for Astrophysics Riccardo Giacconi. In particular, we thank Zoltan Haiman and Massimo Dotti for discussions on optical time-domain searches; Andrew MacFadyen, Alessia Franchini, Magdalena Siwek, and Mark Avara for conversations on binary accretion dynamics; Alessandra De Rosa for an insightful question on ionizing emission; and Jessie Runnoe for slope-side discussions on AGN broad-line regions. C.T. additionally thanks Jonathan Zrake for helpful comments on this manuscript and the anonymous reviewer for an engaging and insightful report. This work was conceived of, performed, and written by humans: C.T., D.O.N., D.J.D. Computation time was supported through the Tycho supercomputer hosted at the SCIENCE HPC center at the University of Copenhagen.\r\nSoftware: Sailfish (J. Zrake & A. MacFadyen 2024), numpy (C. R. Harris et al. 2020), scipy (P. Virtanen et al. 2020), matplotlib (J. D. Hunter 2007), cmasher (E. van der Velden 2020).","supplementarymaterial":"yes","_id":"22964","quality_controlled":"1","publication":"The Astrophysical Journal","das_tickbox":"0","day":"01","citation":{"apa":"Tiede, C., O’Neill, D. W., &#38; D’Orazio, D. J. (2026). Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae914e\">https://doi.org/10.3847/1538-4357/ae914e</a>","ama":"Tiede C, O’Neill DW, D’Orazio DJ. Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks. <i>The Astrophysical Journal</i>. 2026;1008(1). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae914e\">10.3847/1538-4357/ae914e</a>","ieee":"C. Tiede, D. W. O’Neill, and D. J. D’Orazio, “Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks,” <i>The Astrophysical Journal</i>, vol. 1008, no. 1. IOP Publishing, 2026.","ista":"Tiede C, O’Neill DW, D’Orazio DJ. 2026. Dynamics and detectability of long-lived nonaccretion phases for massive Black Hole binaries in cold thermally regulating disks. The Astrophysical Journal. 1008(1), 26.","short":"C. Tiede, D.W. O’Neill, D.J. D’Orazio, The Astrophysical Journal 1008 (2026).","mla":"Tiede, Christopher, et al. “Dynamics and Detectability of Long-Lived Nonaccretion Phases for Massive Black Hole Binaries in Cold Thermally Regulating Disks.” <i>The Astrophysical Journal</i>, vol. 1008, no. 1, 26, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae914e\">10.3847/1538-4357/ae914e</a>.","chicago":"Tiede, Christopher, David W O’Neill, and Daniel J. D’Orazio. “Dynamics and Detectability of Long-Lived Nonaccretion Phases for Massive Black Hole Binaries in Cold Thermally Regulating Disks.” <i>The Astrophysical Journal</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/1538-4357/ae914e\">https://doi.org/10.3847/1538-4357/ae914e</a>."},"publication_status":"published","has_accepted_license":"1","file":[{"checksum":"f3fa2d7a10b75b74290d7a9a68a3d367","relation":"main_file","file_name":"2026_AstrophysicalJour_Tiede.pdf","file_id":"23061","success":1,"date_updated":"2026-10-06T10:44:15Z","file_size":5621643,"content_type":"application/pdf","creator":"dernst","date_created":"2026-10-06T10:44:15Z","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}}]