[{"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"related_material":{"record":[{"id":"19795","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2026-04-07T11:48:07Z","supervisor":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl"}],"doi":"10.15479/AT-ISTA-20206","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"oa_version":"Published Version","file_date_updated":"2025-08-25T13:49:56Z","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-08-25T13:49:55Z","relation":"source_file","file_id":"20228","file_size":39735535,"file_name":"2025_Vorlaufer_Jakob_Thesis.docx","creator":"jvorlauf","date_updated":"2025-08-25T13:49:55Z","access_level":"closed","checksum":"191db3367c19c9b32b65f4bc3a7c19de"},{"creator":"jvorlauf","file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","file_size":10947446,"file_id":"20229","checksum":"104400e6036921569610230c1d4899dc","access_level":"open_access","date_updated":"2025-08-25T13:49:56Z","date_created":"2025-08-25T13:49:56Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"_id":"20206","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"ddc":["621","535"],"year":"2025","publisher":"Institute of Science and Technology Austria","type":"dissertation","date_created":"2025-08-22T08:12:55Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2025-08-25T00:00:00Z","status":"public","degree_awarded":"PhD","day":"25","abstract":[{"lang":"eng","text":"The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. \r\nThe spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions.\r\n"}],"OA_place":"publisher","corr_author":"1","publication_status":"published","title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","has_accepted_license":"1","month":"08","publication_identifier":{"issn":["2663-337X"]},"oa":1,"acknowledgement":"The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989), as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary Project Committee. ","project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer"}],"article_processing_charge":"No","citation":{"ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","mla":"Vorlaufer, Jakob. Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20206.","chicago":"Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20206.","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria.","ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:10.15479/AT-ISTA-20206","apa":"Vorlaufer, J. (2025). Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20206","short":"J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025."},"page":"107"},{"date_updated":"2026-04-14T08:16:57Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17425"}]},"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"file_date_updated":"2025-08-26T10:43:30Z","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"_id":"20212","file":[{"date_updated":"2025-08-26T09:03:50Z","access_level":"closed","checksum":"3331f76bbef74ff4908e2d2c9262045c","file_id":"20230","file_size":32887334,"file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.docx","creator":"omiranda","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-08-26T09:03:50Z"},{"checksum":"02509d50cff8e35c5bcbf71e8d658176","date_updated":"2025-08-26T10:43:30Z","access_level":"closed","creator":"omiranda","embargo_to":"open_access","file_id":"20231","embargo":"2026-08-26","file_name":"2025_MirandaRomero_OsvaldoAntonio_Thesis.pdf","file_size":28636240,"relation":"main_file","content_type":"application/pdf","date_created":"2025-08-26T09:05:55Z"}],"supervisor":[{"last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"doi":"10.15479/AT-ISTA-20212","type":"dissertation","publisher":"Institute of Science and Technology Austria","ddc":["570"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"year":"2025","status":"public","date_published":"2025-08-22T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2025-08-22T14:07:00Z","keyword":["Pten","mtor","cortical development","MADM","Mapk"],"day":"22","degree_awarded":"PhD","OA_place":"publisher","has_accepted_license":"1","corr_author":"1","title":"Unraveling the role of Pten in cortical stem cell lineage progression using MADM","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-063-3"]},"month":"08","author":[{"orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","first_name":"Osvaldo"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"26253","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development"}],"page":"119","article_processing_charge":"No","citation":{"chicago":"Miranda, Osvaldo. “Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20212.","ista":"Miranda O. 2025. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria.","ama":"Miranda O. Unraveling the role of Pten in cortical stem cell lineage progression using MADM. 2025. doi:10.15479/AT-ISTA-20212","apa":"Miranda, O. (2025). Unraveling the role of Pten in cortical stem cell lineage progression using MADM. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20212","short":"O. Miranda, Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM, Institute of Science and Technology Austria, 2025.","mla":"Miranda, Osvaldo. Unraveling the Role of Pten in Cortical Stem Cell Lineage Progression Using MADM. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20212.","ieee":"O. Miranda, “Unraveling the role of Pten in cortical stem cell lineage progression using MADM,” Institute of Science and Technology Austria, 2025."},"acknowledgement":"I would also like to\r\nthank the Austrian Academy of Sciences for awarding me a 2-year DOC fellowship\r\n(DOC26253)."},{"acknowledgement":"The authors thank R. Cooper, G. Yang, V. Kokorev, D. Wen, C. Williams, and H. Übler for useful discussions and comments.\r\nE.I. and K.I.C. acknowledge funding from the Netherlands Research School for Astronomy (NOVA). K.I.C. acknowledges funding from the Dutch Research Council (NWO) through the award of the Vici grant VI.C.212.036. A.A.-H. acknowledges support from grant PID2021-124665NB-I00 funded by MCIN/AEI/10.13039/ 501100011033 and by “ERDF A way of making Europe.” P.G.P.-G. acknowledges support from grant PID2022-139567NB-I00 funded by the Spanish Ministerio de Ciencia e Innovación MCIN/AEI/10.13039/501100011033, FEDER Una manera de hacer Europa. J.A.-M., A.C.-G., and L.C. acknowledge support by grant PIB2021-127718NB-100 from the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe.” L.C. thanks the support from the Cosmic Dawn Center received during visits to DAWN as an international associate. L.C. acknowledges support by grants PIB2021-127718NB-100 and PID2022-139567NB-I00 from the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe.” T.R.G. acknowledges support from the Carlsberg Foundation (grant No. CF20-0534). S.G. acknowledges financial support from the Cosmic Dawn Center (DAWN), funded by the Danish National Research Foundation (DNRF) under grant No. 140. This work was supported by research grants (VIL16599, VIL54489) from VILLUM FONDEN. J.P.P. and T.V.T. acknowledge financial support from the UK Science and Technology Facilities Council and the UK Space Agency.\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the MAST at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs GO #1963, GO #1895, and GTO #1283. The authors acknowledge the team led by co-PIs: C. Williams, M. Maseda, and S. Tacchella, and PI P. Oesch, for developing their respective observing programs with a zero-exclusive-access period. Also based on observations made with the NASA/ESA HST obtained from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. The work presented here is the effort of the entire MIRI team, and the enthusiasm within the MIRI partnership is a significant factor in its success. MIRI draws on the scientific and technical expertise of the following organizations: Ames Research Center, USA; Airbus Defence and Space, UK; CEA-Irfu, Saclay, France; Centre Spatial de Liège, Belgium; Consejo Superior de Investigaciones Científicas, Spain; Carl Zeiss Optronics, Germany; Chalmers University of Technology, Sweden; Danish Space Research Institute, Denmark; Dublin Institute for Advanced Studies, Ireland; European Space Agency, Netherlands; ETCA, Belgium; ETH Zurich, Switzerland; Goddard Space Flight Center, USA; Institute d’Astrophysique Spatiale, France; Instituto Nacional de Técnica Aeroespacial, Spain; Institute for Astronomy, Edinburgh, UK; Jet Propulsion Laboratory, USA; Laboratoire d’Astrophysique de Marseille (LAM), France; Leiden University, Netherlands; Lockheed Advanced Technology Center (USA); NOVA Opt-IR group at Dwingeloo, Netherlands; Northrop Grumman, USA; Max-Planck Institut für Astronomie (MPIA), Heidelberg, Germany; Laboratoire d’Etudes Spatiales et d’Instrumentation en Astrophysique (LESIA), France; Paul Scherrer Institut, Switzerland; Raytheon Vision Systems, USA; RUAG Aerospace, Switzerland; Rutherford Appleton Laboratory (RAL Space), UK; Space Telescope Science Institute, USA; Toegepast-Natuurwetenschappelijk Onderzoek (TNO-TPD), Netherlands; UK Astronomy Technology Centre, UK; University College London, UK; University of Amsterdam, Netherlands; University of Arizona, USA; University of Cardiff, UK; University of Cologne, Germany; University of Ghent; University of Groningen, Netherlands; University of Leicester, UK; University of Leuven, Belgium; University of Stockholm, Sweden; Utah State University, USA.\r\nFor the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to the Author Accepted Manuscript version arising from this submission.","arxiv":1,"oa":1,"isi":1,"article_processing_charge":"Yes","citation":{"short":"E. Iani, P. Rinaldi, K.I. Caputi, M. Annunziatella, D. Langeroodi, J. Melinder, P.G. Pérez-González, J. Álvarez-Márquez, L.A. Boogaard, S.E.I. Bosman, L. Costantin, T. Moutard, L. Colina, G. Östlin, T.R. Greve, G. Wright, A. Alonso-Herrero, A. Bik, S. Gillman, A. Crespo Gómez, J. Hjorth, S. Kendrew, A. Labiano, J.P. Pye, T.V. Tikkanen, F. Walter, M. Güdel, T. Henning, P.P. Van Der Werf, The Astrophysical Journal 989 (2025).","apa":"Iani, E., Rinaldi, P., Caputi, K. I., Annunziatella, M., Langeroodi, D., Melinder, J., … Van Der Werf, P. P. (2025). MIDIS: MIRI uncovers Virgil, the first Little Red Dot with clear detection of its host galaxy at z ≃ 6.6. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ade5a6","ama":"Iani E, Rinaldi P, Caputi KI, et al. MIDIS: MIRI uncovers Virgil, the first Little Red Dot with clear detection of its host galaxy at z ≃ 6.6. The Astrophysical Journal. 2025;989(2). doi:10.3847/1538-4357/ade5a6","chicago":"Iani, Edoardo, Pierluigi Rinaldi, Karina I. Caputi, Marianna Annunziatella, Danial Langeroodi, Jens Melinder, Pablo G. Pérez-González, et al. “MIDIS: MIRI Uncovers Virgil, the First Little Red Dot with Clear Detection of Its Host Galaxy at z ≃ 6.6.” The Astrophysical Journal. IOP Publishing, 2025. https://doi.org/10.3847/1538-4357/ade5a6.","ista":"Iani E, Rinaldi P, Caputi KI, Annunziatella M, Langeroodi D, Melinder J, Pérez-González PG, Álvarez-Márquez J, Boogaard LA, Bosman SEI, Costantin L, Moutard T, Colina L, Östlin G, Greve TR, Wright G, Alonso-Herrero A, Bik A, Gillman S, Crespo Gómez A, Hjorth J, Kendrew S, Labiano A, Pye JP, Tikkanen TV, Walter F, Güdel M, Henning T, Van Der Werf PP. 2025. MIDIS: MIRI uncovers Virgil, the first Little Red Dot with clear detection of its host galaxy at z ≃ 6.6. The Astrophysical Journal. 989(2), 160.","mla":"Iani, Edoardo, et al. “MIDIS: MIRI Uncovers Virgil, the First Little Red Dot with Clear Detection of Its Host Galaxy at z ≃ 6.6.” The Astrophysical Journal, vol. 989, no. 2, 160, IOP Publishing, 2025, doi:10.3847/1538-4357/ade5a6.","ieee":"E. Iani et al., “MIDIS: MIRI uncovers Virgil, the first Little Red Dot with clear detection of its host galaxy at z ≃ 6.6,” The Astrophysical Journal, vol. 989, no. 2. IOP Publishing, 2025."},"language":[{"iso":"eng"}],"author":[{"full_name":"Iani, Edoardo","orcid":"0000-0001-8386-3546","id":"4053390a-6b68-11ef-9828-a3b8adef8d0a","first_name":"Edoardo","last_name":"Iani"},{"full_name":"Rinaldi, Pierluigi","last_name":"Rinaldi","first_name":"Pierluigi"},{"last_name":"Caputi","first_name":"Karina I.","full_name":"Caputi, Karina I."},{"first_name":"Marianna","last_name":"Annunziatella","full_name":"Annunziatella, Marianna"},{"first_name":"Danial","last_name":"Langeroodi","full_name":"Langeroodi, Danial"},{"full_name":"Melinder, Jens","last_name":"Melinder","first_name":"Jens"},{"full_name":"Pérez-González, Pablo G.","last_name":"Pérez-González","first_name":"Pablo G."},{"full_name":"Álvarez-Márquez, Javier","last_name":"Álvarez-Márquez","first_name":"Javier"},{"last_name":"Boogaard","first_name":"Leindert A.","full_name":"Boogaard, Leindert A."},{"first_name":"Sarah E.I.","last_name":"Bosman","full_name":"Bosman, Sarah E.I."},{"first_name":"Luca","last_name":"Costantin","full_name":"Costantin, Luca"},{"first_name":"Thibaud","last_name":"Moutard","full_name":"Moutard, Thibaud"},{"last_name":"Colina","first_name":"Luis","full_name":"Colina, Luis"},{"last_name":"Östlin","first_name":"Göran","full_name":"Östlin, Göran"},{"full_name":"Greve, Thomas R.","last_name":"Greve","first_name":"Thomas R."},{"full_name":"Wright, Gillian","last_name":"Wright","first_name":"Gillian"},{"full_name":"Alonso-Herrero, Almudena","first_name":"Almudena","last_name":"Alonso-Herrero"},{"full_name":"Bik, Arjan","first_name":"Arjan","last_name":"Bik"},{"first_name":"Steven","last_name":"Gillman","full_name":"Gillman, Steven"},{"full_name":"Crespo Gómez, Alejandro","first_name":"Alejandro","last_name":"Crespo Gómez"},{"full_name":"Hjorth, Jens","first_name":"Jens","last_name":"Hjorth"},{"full_name":"Kendrew, Sarah","first_name":"Sarah","last_name":"Kendrew"},{"full_name":"Labiano, Alvaro","first_name":"Alvaro","last_name":"Labiano"},{"full_name":"Pye, John P.","last_name":"Pye","first_name":"John P."},{"full_name":"Tikkanen, Tuomo V.","last_name":"Tikkanen","first_name":"Tuomo V."},{"last_name":"Walter","first_name":"Fabian","full_name":"Walter, Fabian"},{"full_name":"Güdel, Manuel","last_name":"Güdel","first_name":"Manuel"},{"full_name":"Henning, Thomas","first_name":"Thomas","last_name":"Henning"},{"full_name":"Van Der Werf, Paul P.","last_name":"Van Der Werf","first_name":"Paul P."}],"month":"08","scopus_import":"1","volume":989,"publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"OA_type":"gold","publication_status":"published","title":"MIDIS: MIRI uncovers Virgil, the first Little Red Dot with clear detection of its host galaxy at z ≃ 6.6","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We present Virgil, a Mid-Infrared Instrument (MIRI) extremely red object detected with the F1000W filter as part of the MIRI Deep Imaging Survey observations of the Hubble Ultra Deep Field. Virgil is an Lyα emitter (LAE) at zspec = 6.6312 ± 0.0019 (from the Very Large Telescope/MUSE) with a rest-frame UV-to-optical spectral energy distribution (SED) typical of LAEs at similar redshifts. However, MIRI observations reveal an unexpected extremely red color at rest-frame near-infrared (NIR) wavelengths, F444W − F1000W = 2.33 ± 0.06. Such a steep\r\nrise in the NIR, completely missed without MIRI imaging, is poorly reproduced by models including only stellar populations and hints toward the presence of an active galactic nucleus, although alternative explanations such as extreme dust obscuration and strong nebular continuum and emission lines contribution due to young stellar ages cannot be completely ruled out. According to the shape of its overall SED, Virgil belongs to the recently discovered\r\npopulation of little red dots but displays an extended rest-frame UV-optical wavelength morphology following a 2DSérsic profile with an average index of n = 0.93+0.85_0.31 and re = 0.49+0.05_0.11 pkpc. Only at MIRI wavelengths, Virgil is unresolved due to the coarser point-spread function. This discovery demonstrates the crucial importance of deep MIRI surveys to reveal the true nature and properties of high-z galaxies that otherwise would be misinterpreted and raises the question of how common Virgil-like objects could be in the early Universe."}],"intvolume":" 989","OA_place":"publisher","publication":"The Astrophysical Journal","quality_controlled":"1","day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-24T22:01:29Z","date_published":"2025-08-20T00:00:00Z","status":"public","year":"2025","issue":"2","ddc":["520"],"publisher":"IOP Publishing","article_type":"original","type":"journal_article","doi":"10.3847/1538-4357/ade5a6","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"PlanS_conform":"1","_id":"20217","article_number":"160","file":[{"relation":"main_file","date_created":"2025-09-02T06:40:23Z","content_type":"application/pdf","success":1,"checksum":"92196e8352dddb1f305c253da1996ab6","access_level":"open_access","date_updated":"2025-09-02T06:40:23Z","creator":"dernst","file_size":5474992,"file_name":"2025_AstrophysicalJour_Iani.pdf","file_id":"20268"}],"oa_version":"Published Version","file_date_updated":"2025-09-02T06:40:23Z","DOAJ_listed":"1","department":[{"_id":"JoMa"}],"date_updated":"2026-02-16T12:43:12Z","external_id":{"arxiv":["2406.18207"],"isi":["001548132000001"]}},{"acknowledgement":"Living Architecture is Funded by the EU Horizon 2020 Future Emerging Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6 collaborating institutions—Newcastle University, University of Trento, University of the West of England, Spanish National Research Council, Explora Biotech and Liquifer Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE) project is funded by an EU Innovation Award for the development of a bio-digital ‘brick’ prototype, a collaboration between Newcastle University, Translating Nature, and the University of the West of England (2019–2021) under EU Grant Agreement No. 851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy) is Funded by the European Union under Grant Agreement Number 101114746, which is a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton (UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish National Research Council (Spain), and Associated Partners, the University of the West of England (UK) and University of Southampton (UK). Mi-Hy is also supported through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL).","arxiv":1,"oa":1,"citation":{"mla":"Volpe, Giorgio, et al. “Roadmap for Animate Matter.” Journal of Physics Condensed Matter, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:10.1088/1361-648X/adebd3.","ieee":"G. Volpe et al., “Roadmap for animate matter,” Journal of Physics Condensed Matter, vol. 37, no. 33. IOP Publishing, 2025.","short":"G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J. Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng, D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth, C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani, T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong, D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong, Journal of Physics Condensed Matter 37 (2025).","chicago":"Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.” Journal of Physics Condensed Matter. IOP Publishing, 2025. https://doi.org/10.1088/1361-648X/adebd3.","ista":"Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J, Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal of Physics Condensed Matter. 37(33), 333501.","ama":"Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. Journal of Physics Condensed Matter. 2025;37(33). doi:10.1088/1361-648X/adebd3","apa":"Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez, L., … Armstrong, R. (2025). Roadmap for animate matter. Journal of Physics Condensed Matter. IOP Publishing. https://doi.org/10.1088/1361-648X/adebd3"},"isi":1,"article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"author":[{"full_name":"Volpe, Giorgio","last_name":"Volpe","first_name":"Giorgio"},{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"last_name":"Guix","first_name":"Maria","full_name":"Guix, Maria"},{"first_name":"Mark","last_name":"Miodownik","full_name":"Miodownik, Mark"},{"first_name":"Nicolas","last_name":"Martin","full_name":"Martin, Nicolas"},{"first_name":"Laura","last_name":"Alvarez","full_name":"Alvarez, Laura"},{"first_name":"Juliane","last_name":"Simmchen","full_name":"Simmchen, Juliane"},{"full_name":"Leonardo, Roberto Di","first_name":"Roberto Di","last_name":"Leonardo"},{"full_name":"Pellicciotta, Nicola","first_name":"Nicola","last_name":"Pellicciotta"},{"id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","first_name":"Quentin","last_name":"Martinet","full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632"},{"last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"},{"last_name":"Ng","first_name":"Wai Kit","full_name":"Ng, Wai Kit"},{"full_name":"Saxena, Dhruv","last_name":"Saxena","first_name":"Dhruv"},{"full_name":"Sapienza, Riccardo","first_name":"Riccardo","last_name":"Sapienza"},{"first_name":"Sara","last_name":"Nadine","full_name":"Nadine, Sara"},{"full_name":"Mano, João F.","first_name":"João F.","last_name":"Mano"},{"full_name":"Mahdavi, Reza","last_name":"Mahdavi","first_name":"Reza"},{"first_name":"Caroline","last_name":"Beck Adiels","full_name":"Beck Adiels, Caroline"},{"full_name":"Forth, Joe","first_name":"Joe","last_name":"Forth"},{"full_name":"Santangelo, Christian","first_name":"Christian","last_name":"Santangelo"},{"first_name":"Stefano","last_name":"Palagi","full_name":"Palagi, Stefano"},{"last_name":"Seok","first_name":"Ji Min","full_name":"Seok, Ji Min"},{"first_name":"Victoria A.","last_name":"Webster-Wood","full_name":"Webster-Wood, Victoria A."},{"full_name":"Wang, Shuhong","last_name":"Wang","first_name":"Shuhong"},{"full_name":"Yao, Lining","last_name":"Yao","first_name":"Lining"},{"first_name":"Amirreza","last_name":"Aghakhani","full_name":"Aghakhani, Amirreza"},{"first_name":"Thomas","last_name":"Barois","full_name":"Barois, Thomas"},{"full_name":"Kellay, Hamid","last_name":"Kellay","first_name":"Hamid"},{"full_name":"Coulais, Corentin","last_name":"Coulais","first_name":"Corentin"},{"full_name":"Van Hecke, Martin","first_name":"Martin","last_name":"Van Hecke"},{"full_name":"Pierce, Christopher J.","last_name":"Pierce","first_name":"Christopher J."},{"full_name":"Wang, Tianyu","last_name":"Wang","first_name":"Tianyu"},{"full_name":"Chong, Baxi","first_name":"Baxi","last_name":"Chong"},{"first_name":"Daniel I.","last_name":"Goldman","full_name":"Goldman, Daniel I."},{"full_name":"Reina, Andreagiovanni","last_name":"Reina","first_name":"Andreagiovanni"},{"first_name":"Vito","last_name":"Trianni","full_name":"Trianni, Vito"},{"first_name":"Giovanni","last_name":"Volpe","full_name":"Volpe, Giovanni"},{"full_name":"Beckett, Richard","first_name":"Richard","last_name":"Beckett"},{"full_name":"Nair, Sean P.","first_name":"Sean P.","last_name":"Nair"},{"last_name":"Armstrong","first_name":"Rachel","full_name":"Armstrong, Rachel"}],"month":"08","scopus_import":"1","volume":37,"publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"OA_type":"hybrid","publication_status":"published","title":"Roadmap for animate matter","has_accepted_license":"1","abstract":[{"text":"Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner.","lang":"eng"}],"intvolume":" 37","publication":"Journal of Physics Condensed Matter","OA_place":"publisher","quality_controlled":"1","day":"18","date_created":"2025-08-24T22:01:30Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-08-18T00:00:00Z","status":"public","year":"2025","issue":"33","ddc":["530"],"publisher":"IOP Publishing","type":"journal_article","article_type":"original","doi":"10.1088/1361-648X/adebd3","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"PlanS_conform":"1","_id":"20218","file":[{"checksum":"7309274f78bed785b158bd290337f456","date_updated":"2025-09-02T07:22:48Z","access_level":"open_access","creator":"dernst","file_id":"20271","file_size":8997829,"file_name":"2025_CondensedMatter_Volpe.pdf","relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2025-09-02T07:22:48Z"}],"article_number":"333501","oa_version":"Published Version","file_date_updated":"2025-09-02T07:22:48Z","department":[{"_id":"JePa"}],"date_updated":"2025-09-30T14:25:12Z","external_id":{"isi":["001550090200001"],"arxiv":["2407.10623"]}},{"isi":1,"article_processing_charge":"No","citation":{"mla":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface, vol. 22, no. 229, 20250202, The Royal Society, 2025, doi:10.1098/rsif.2025.0202.","ieee":"O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction in bifunctional insects,” Journal of the Royal Society Interface, vol. 22, no. 229. The Royal Society, 2025.","ista":"Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.","chicago":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” Journal of the Royal Society Interface. The Royal Society, 2025. https://doi.org/10.1098/rsif.2025.0202.","ama":"Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 2025;22(229). doi:10.1098/rsif.2025.0202","apa":"Ayalon, O., & Rajendran, H. (2025). Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2025.0202","short":"O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025)."},"language":[{"iso":"eng"}],"author":[{"full_name":"Ayalon, Oran","first_name":"Oran","last_name":"Ayalon"},{"full_name":"Rajendran, Harikrishnan","last_name":"Rajendran","id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416","first_name":"Harikrishnan"}],"acknowledgement":"We acknowledge Prof. Uri Alon for introducing us to the topic of systems biology during the graduate course at the Weizmann Institute of Science, whose insights and teachings have greatly inspired this work.","publication_identifier":{"issn":["1742-5689"],"eissn":["1742-5662"]},"month":"08","scopus_import":"1","volume":22,"publication_status":"published","title":"Interplay of asexual and sexual reproduction in bifunctional insects","corr_author":"1","intvolume":" 22","abstract":[{"text":"Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.","lang":"eng"}],"publication":"Journal of the Royal Society Interface","OA_type":"closed access","quality_controlled":"1","day":"13","date_published":"2025-08-13T00:00:00Z","status":"public","date_created":"2025-08-24T22:01:30Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"The Royal Society","type":"journal_article","article_type":"original","year":"2025","pmid":1,"issue":"229","_id":"20219","article_number":"20250202","oa_version":"None","doi":"10.1098/rsif.2025.0202","date_updated":"2025-09-30T14:24:40Z","external_id":{"pmid":["40799050"],"isi":["001548084900001"]},"department":[{"_id":"SyCr"}]},{"has_accepted_license":"1","publication_status":"published","title":"The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat","publication":"Science Advances","OA_place":"publisher","abstract":[{"text":"Stress granules (SG) are biomolecular condensates that represent an adaptive response of cells to various stresses, including heat. However, the cell type–specific function and relevance of SG formation, especially during reproductive development, are largely not understood. Here, we show that the meiotic A-type cyclin TARDY ASYNCHRONOUS MEIOSIS (TAM) is recruited to SGs in male meiocytes of Arabidopsis after exposure to heat. We find that the amino terminus of TAM is necessary and sufficient for the localization of proteins to meiotic SGs. Swapping the amino terminus of TAM with the one of its sister protein CYCA1;1 resulted in a separation-of-function allele of TAM, which prevents the partitioning of TAM to SGs while restoring a wild-type phenotype in a tam mutant background under nonheat stress conditions. Notably, plants expressing this TAM version prematurely terminate meiosis under heat resulting in unreduced gametes. Thus, the formation of TAM-containing SGs is necessary for genome stability under heat stress.","lang":"eng"}],"intvolume":" 11","OA_type":"gold","ec_funded":1,"quality_controlled":"1","day":"08","page":"eadr5694","isi":1,"article_processing_charge":"Yes","citation":{"ieee":"J. G. De Jaeger-Braet et al., “The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat,” Science Advances, vol. 11, no. 32. AAAS, p. eadr5694, 2025.","mla":"De Jaeger-Braet, Joke G., et al. “The Recruitment of the A-Type Cyclin TAM to Stress Granules Is Crucial for Meiotic Fidelity under Heat.” Science Advances, vol. 11, no. 32, AAAS, 2025, p. eadr5694, doi:10.1126/sciadv.adr5694.","ama":"De Jaeger-Braet JG, Hartmann M, Böttger L, et al. The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science Advances. 2025;11(32):eadr5694. doi:10.1126/sciadv.adr5694","apa":"De Jaeger-Braet, J. G., Hartmann, M., Böttger, L., Yang, C., Hamada, T., Hoth, S., … Schnittger, A. (2025). The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science Advances. AAAS. https://doi.org/10.1126/sciadv.adr5694","ista":"De Jaeger-Braet JG, Hartmann M, Böttger L, Yang C, Hamada T, Hoth S, Feng X, Weingartner M, Schnittger A. 2025. The recruitment of the A-type cyclin TAM to stress granules is crucial for meiotic fidelity under heat. Science Advances. 11(32), eadr5694.","chicago":"De Jaeger-Braet, Joke G, Merle Hartmann, Lev Böttger, Chao Yang, Takahiro Hamada, Stefan Hoth, Xiaoqi Feng, Magdalena Weingartner, and Arp Schnittger. “The Recruitment of the A-Type Cyclin TAM to Stress Granules Is Crucial for Meiotic Fidelity under Heat.” Science Advances. AAAS, 2025. https://doi.org/10.1126/sciadv.adr5694.","short":"J.G. De Jaeger-Braet, M. Hartmann, L. Böttger, C. Yang, T. Hamada, S. Hoth, X. Feng, M. Weingartner, A. Schnittger, Science Advances 11 (2025) eadr5694."},"author":[{"full_name":"De Jaeger-Braet, Joke G","last_name":"De Jaeger-Braet","id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","first_name":"Joke G"},{"first_name":"Merle","last_name":"Hartmann","full_name":"Hartmann, Merle"},{"full_name":"Böttger, Lev","last_name":"Böttger","first_name":"Lev"},{"last_name":"Yang","first_name":"Chao","id":"082e3e6e-8069-11ed-8390-c8cce7b1aaca","full_name":"Yang, Chao"},{"first_name":"Takahiro","last_name":"Hamada","full_name":"Hamada, Takahiro"},{"full_name":"Hoth, Stefan","first_name":"Stefan","last_name":"Hoth"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Weingartner, Magdalena","last_name":"Weingartner","first_name":"Magdalena"},{"full_name":"Schnittger, Arp","first_name":"Arp","last_name":"Schnittger"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"acknowledgement":"We thank L. Strader (Duke University, Durham) and A. Holehouse (Washington University, Saint Louis) for discussion and input in LLPS. We thank T. Nakagawa (Shimane University, Matsue) for providing the pGWB604 Gateway vector containing bar gene identified by Meiji Seika Kaisha Ltd. We thank M. Heese (Hamburg University) for the critical reading and comments on this manuscript. We further thank J. Mehrmann (Hamburg University) for technical assistance. We thank the ISTA imaging facility for assistance for microscopy.\r\nThis project has received funding from JST-PRESTO (JPMJPR18H7), JST-CREST (JPMJCR18H4), European Union’s Horizon 2020 under MSCA grant 101034413, and a federal grant from the state of Hamburg (LFF-BiCon).","oa":1,"publication_identifier":{"eissn":["2375-2548"]},"volume":11,"scopus_import":"1","month":"08","file":[{"file_name":"2025_ScienceAdvance_DeJaegerBraet.pdf","file_size":10876817,"file_id":"20270","creator":"dernst","access_level":"open_access","date_updated":"2025-09-02T07:05:37Z","checksum":"0f1ae246acc9b075f01bf4afe382c8ba","date_created":"2025-09-02T07:05:37Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"_id":"20220","DOAJ_listed":"1","file_date_updated":"2025-09-02T07:05:37Z","oa_version":"Published Version","doi":"10.1126/sciadv.adr5694","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"date_updated":"2025-09-30T14:24:10Z","external_id":{"isi":["001549102600016"]},"department":[{"_id":"XiFe"}],"status":"public","date_published":"2025-08-08T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-08-24T22:01:30Z","article_type":"original","type":"journal_article","publisher":"AAAS","year":"2025","ddc":["580"],"acknowledged_ssus":[{"_id":"Bio"}],"issue":"32"},{"file":[{"creator":"dernst","file_size":3212706,"file_name":"2025_NanoLetters_Shi.pdf","file_id":"20269","checksum":"bfc167d8904c0c47c3de2a8d0ec699d5","access_level":"open_access","date_updated":"2025-09-02T06:50:11Z","date_created":"2025-09-02T06:50:11Z","success":1,"content_type":"application/pdf","relation":"main_file"}],"_id":"20221","oa_version":"Published Version","file_date_updated":"2025-09-02T06:50:11Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1021/acs.nanolett.5c03693","PlanS_conform":"1","date_updated":"2025-09-30T14:23:39Z","external_id":{"isi":["001537145800001"],"pmid":["40707400"]},"department":[{"_id":"LaVe"}],"date_published":"2025-07-24T00:00:00Z","status":"public","date_created":"2025-08-24T22:01:30Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Chemical Society","article_type":"original","type":"journal_article","year":"2025","pmid":1,"issue":"31","ddc":["540"],"publication_status":"published","title":"Single-molecule conductance through hybrid radially and linearly π-conjugated macromolecules reveals an unusual intramolecular π-interaction","corr_author":"1","has_accepted_license":"1","intvolume":" 25","abstract":[{"lang":"eng","text":"We describe the design, synthesis, and single-molecule junction conductance of π-electron molecules bearing both radial and linear π-conjugation pathways, whereby cycloparaphenylene (CPP) radial cores are π-extended linearly with aryl alkyne substituents as models for previously reported CPP-arylene ethynylene conjugated polymers. Although radially and linearly conjugated molecules have been studied previously in isolation as junction-bridging molecular electronic units, this is the first study to examine molecules where both topologies are operative. Our results reveal that the presence of radial CPP components within the junction-spanning pathway leads to a reduction in the conductance of the backbone compared to model linear phenyl substituents. Through tight-binding and DFT-based calculations, we attribute this conductance change to intramolecular van der Waals (vdW) interactions between the CPP ring and the junction-spanning arylene-ethynylene molecular backbone. These interactions induce changes in the dihedral angles of the backbone, leading to a reduced overlap of π orbitals within the molecular junction."}],"publication":"Nano Letters","OA_place":"publisher","OA_type":"hybrid","quality_controlled":"1","day":"24","isi":1,"citation":{"mla":"Shi, Wanzhuo, et al. “Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction.” Nano Letters, vol. 25, no. 31, American Chemical Society, 2025, pp. 12101–06, doi:10.1021/acs.nanolett.5c03693.","ieee":"W. Shi, M. Wang, L. Venkataraman, and J. D. Tovar, “Single-molecule conductance through hybrid radially and linearly π-conjugated macromolecules reveals an unusual intramolecular π-interaction,” Nano Letters, vol. 25, no. 31. American Chemical Society, pp. 12101–12106, 2025.","short":"W. Shi, M. Wang, L. Venkataraman, J.D. Tovar, Nano Letters 25 (2025) 12101–12106.","apa":"Shi, W., Wang, M., Venkataraman, L., & Tovar, J. D. (2025). Single-molecule conductance through hybrid radially and linearly π-conjugated macromolecules reveals an unusual intramolecular π-interaction. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.5c03693","ama":"Shi W, Wang M, Venkataraman L, Tovar JD. Single-molecule conductance through hybrid radially and linearly π-conjugated macromolecules reveals an unusual intramolecular π-interaction. Nano Letters. 2025;25(31):12101-12106. doi:10.1021/acs.nanolett.5c03693","chicago":"Shi, Wanzhuo, Mengjiao Wang, Latha Venkataraman, and John D. Tovar. “Single-Molecule Conductance through Hybrid Radially and Linearly π-Conjugated Macromolecules Reveals an Unusual Intramolecular π-Interaction.” Nano Letters. American Chemical Society, 2025. https://doi.org/10.1021/acs.nanolett.5c03693.","ista":"Shi W, Wang M, Venkataraman L, Tovar JD. 2025. Single-molecule conductance through hybrid radially and linearly π-conjugated macromolecules reveals an unusual intramolecular π-interaction. Nano Letters. 25(31), 12101–12106."},"article_processing_charge":"Yes (via OA deal)","page":"12101-12106","language":[{"iso":"eng"}],"author":[{"last_name":"Shi","id":"a3010425-87c8-11f0-8106-bec32bea74da","first_name":"Wanzhuo","full_name":"Shi, Wanzhuo"},{"first_name":"Mengjiao","last_name":"Wang","full_name":"Wang, Mengjiao"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","last_name":"Venkataraman","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089"},{"last_name":"Tovar","first_name":"John D.","full_name":"Tovar, John D."}],"acknowledgement":"We thank Prof. Volker Blum for useful discussions. We thank the Department of Energy Office of Basic Energy Science (DE-SC0019017) and the National Science Foundation (NSF-DMR 2241180) for supporting this research. This work was supported in part by the Institute of Science and Technology Austria.","oa":1,"publication_identifier":{"eissn":["1530-6992"]},"month":"07","scopus_import":"1","volume":25},{"quality_controlled":"1","day":"01","OA_type":"gold","has_accepted_license":"1","title":"An extension of Muller's sheltering hypothesis for the evolution of sex chromosome gene content","publication_status":"published","OA_place":"publisher","publication":"Molecular Biology and Evolution","intvolume":" 42","abstract":[{"text":"The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become “sheltered” from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favor in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Muller's hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e. selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss.","lang":"eng"}],"volume":42,"month":"08","scopus_import":"1","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"acknowledgement":"We thank Filip Ruzicka, Colin Olito, Akane Uesugi, Melissa Toups, Daniel Jeffries, the Associate Editor, and anonymous reviewers, for comments and suggestions on earlier versions of the paper. We are particularly grateful to Deborah Charlesworth and Brian Charlesworth for extensive comments on two different drafts of the manuscript. We also thank Aneil Agrawal and Thomas Lenormand for email correspondence about the data on dominance and ways to interpret it. Technical support was provided by ISTA Scientific Computing Unit.","oa":1,"citation":{"chicago":"Mrnjavac, Andrea, Beatriz Vicoso, and Tim Connallon. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” Molecular Biology and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf177.","ista":"Mrnjavac A, Vicoso B, Connallon T. 2025. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 42(8), msaf177.","ama":"Mrnjavac A, Vicoso B, Connallon T. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 2025;42(8). doi:10.1093/molbev/msaf177","apa":"Mrnjavac, A., Vicoso, B., & Connallon, T. (2025). An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msaf177","short":"A. Mrnjavac, B. Vicoso, T. Connallon, Molecular Biology and Evolution 42 (2025).","mla":"Mrnjavac, Andrea, et al. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” Molecular Biology and Evolution, vol. 42, no. 8, msaf177, Oxford University Press, 2025, doi:10.1093/molbev/msaf177.","ieee":"A. Mrnjavac, B. Vicoso, and T. Connallon, “An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content,” Molecular Biology and Evolution, vol. 42, no. 8. Oxford University Press, 2025."},"isi":1,"article_processing_charge":"Yes","author":[{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"last_name":"Connallon","first_name":"Tim","full_name":"Connallon, Tim"}],"language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"date_updated":"2025-09-30T14:25:57Z","related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/xydegenerate"}]},"external_id":{"pmid":["40713898"],"isi":["001547617100001"]},"doi":"10.1093/molbev/msaf177","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"PlanS_conform":"1","article_number":"msaf177","_id":"20223","file":[{"relation":"main_file","date_created":"2025-09-02T07:47:32Z","content_type":"application/pdf","success":1,"checksum":"f40abffa56cb1e9ff65800f2a7d7b39a","access_level":"open_access","date_updated":"2025-09-02T07:47:32Z","creator":"dernst","file_size":1239841,"file_name":"2025_MolecularBioEvolution_Mrnjavac.pdf","file_id":"20274"}],"DOAJ_listed":"1","file_date_updated":"2025-09-02T07:47:32Z","oa_version":"Published Version","year":"2025","ddc":["570"],"pmid":1,"issue":"8","acknowledged_ssus":[{"_id":"ScienComp"}],"type":"journal_article","article_type":"original","publisher":"Oxford University Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-08-24T22:01:31Z","status":"public","date_published":"2025-08-01T00:00:00Z"},{"publisher":"Association for Computing Machinery","type":"conference","ddc":["000"],"conference":{"name":"GECCO: Genetic and evolutionary computation conference","start_date":"2025-07-14","location":"Malaga, Spain","end_date":"2025-07-18"},"year":"2025","date_published":"2025-07-13T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-24T22:01:31Z","external_id":{"isi":["001556459900031"]},"date_updated":"2025-12-01T12:35:24Z","department":[{"_id":"DaAl"}],"oa_version":"Published Version","file_date_updated":"2025-09-02T07:41:13Z","_id":"20224","file":[{"file_name":"2025_GECCO_Martynov.pdf","file_size":608996,"file_id":"20273","creator":"dernst","access_level":"open_access","date_updated":"2025-09-02T07:41:13Z","checksum":"7e513fa508cff7e8a0d33f50b1fe09af","date_created":"2025-09-02T07:41:13Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1145/3712256.3726425","publication_identifier":{"isbn":["9798400714658"]},"month":"07","scopus_import":"1","language":[{"iso":"eng"}],"author":[{"full_name":"Martynov, Pavel","first_name":"Pavel","last_name":"Martynov"},{"first_name":"Maxim","last_name":"Buzdalov","full_name":"Buzdalov, Maxim"},{"first_name":"Sergei","id":"f773bf05-72ef-11ef-b75a-a383d22f454b","last_name":"Pankratov","full_name":"Pankratov, Sergei"},{"first_name":"Vitaliy","last_name":"Aksenov","full_name":"Aksenov, Vitaliy"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"isi":1,"article_processing_charge":"Yes (in subscription journal)","citation":{"mla":"Martynov, Pavel, et al. “In the Search of Optimal Tree Networks: Hardness and Heuristics.” Proceedings of the 2025 Genetic and Evolutionary Computation Conference, Association for Computing Machinery, 2025, pp. 249–57, doi:10.1145/3712256.3726425.","ieee":"P. Martynov, M. Buzdalov, S. Pankratov, V. Aksenov, and S. Schmid, “In the search of optimal tree networks: Hardness and heuristics,” in Proceedings of the 2025 Genetic and Evolutionary Computation Conference, Malaga, Spain, 2025, pp. 249–257.","ista":"Martynov P, Buzdalov M, Pankratov S, Aksenov V, Schmid S. 2025. In the search of optimal tree networks: Hardness and heuristics. Proceedings of the 2025 Genetic and Evolutionary Computation Conference. GECCO: Genetic and evolutionary computation conference, 249–257.","chicago":"Martynov, Pavel, Maxim Buzdalov, Sergei Pankratov, Vitaliy Aksenov, and Stefan Schmid. “In the Search of Optimal Tree Networks: Hardness and Heuristics.” In Proceedings of the 2025 Genetic and Evolutionary Computation Conference, 249–57. Association for Computing Machinery, 2025. https://doi.org/10.1145/3712256.3726425.","apa":"Martynov, P., Buzdalov, M., Pankratov, S., Aksenov, V., & Schmid, S. (2025). In the search of optimal tree networks: Hardness and heuristics. In Proceedings of the 2025 Genetic and Evolutionary Computation Conference (pp. 249–257). Malaga, Spain: Association for Computing Machinery. https://doi.org/10.1145/3712256.3726425","ama":"Martynov P, Buzdalov M, Pankratov S, Aksenov V, Schmid S. In the search of optimal tree networks: Hardness and heuristics. In: Proceedings of the 2025 Genetic and Evolutionary Computation Conference. Association for Computing Machinery; 2025:249-257. doi:10.1145/3712256.3726425","short":"P. Martynov, M. Buzdalov, S. Pankratov, V. Aksenov, S. Schmid, in:, Proceedings of the 2025 Genetic and Evolutionary Computation Conference, Association for Computing Machinery, 2025, pp. 249–257."},"page":"249-257","oa":1,"acknowledgement":"Research was supported by the German Research Foundation (DFG), grant 470029389 (FlexNets).","day":"13","quality_controlled":"1","abstract":[{"text":"Traffic in datacenters may follow some pattern: some pairs of servers communicate more frequently than others. Demand-oblivious networks may perform poorly for such workloads, and demand-aware networks optimized for traffic should be used instead. Unfortunately, not all shapes of networks are feasible in real hardware. Practical limitations are usually provided in the form of a topology. For example, a network may be required to be a binary tree, a bounded-degree graph or a Fat tree.\r\nIn this work, we consider a topology of a binary tree, one of the most fundamental network topologies. We show that already finding an optimal demand-aware binary tree network is NP-hard. Then, we explore how various optimization techniques, including simple local searches, as well as deterministic mutation and crossover operators, cope with generating efficient tree networks on real-life and synthetic workloads.","lang":"eng"}],"OA_place":"publisher","publication":"Proceedings of the 2025 Genetic and Evolutionary Computation Conference","title":"In the search of optimal tree networks: Hardness and heuristics","publication_status":"published","has_accepted_license":"1","OA_type":"hybrid"},{"department":[{"_id":"ToHe"}],"external_id":{"isi":["001562506600002"],"arxiv":["2505.18833"]},"date_updated":"2025-12-01T12:34:41Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1007/978-3-031-98679-6_2","file_date_updated":"2025-09-02T07:34:33Z","oa_version":"Published Version","alternative_title":["LNCS"],"_id":"20225","file":[{"relation":"main_file","date_created":"2025-09-02T07:34:33Z","success":1,"content_type":"application/pdf","access_level":"open_access","date_updated":"2025-09-02T07:34:33Z","checksum":"beb1e2637de5b2268cc2262119439113","file_name":"2025_CAV_HenzingerT.pdf","file_size":884831,"file_id":"20272","creator":"dernst"}],"ddc":["000"],"year":"2025","conference":{"name":"CAV: Computer Aided Verification","start_date":"2025-07-23","end_date":"2025-07-25","location":"Zagreb, Croatia"},"type":"conference","publisher":"Springer Nature","date_created":"2025-08-24T22:01:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2025-07-22T00:00:00Z","day":"22","quality_controlled":"1","ec_funded":1,"OA_type":"hybrid","OA_place":"publisher","publication":"37th International Conference on Computer Aided Verification","abstract":[{"text":"We present the first supermartingale certificate for quantitative \r\n-regular properties of discrete-time infinite-state stochastic systems. Our certificate is defined on the product of the stochastic system and a limit-deterministic Büchi automaton that specifies the property of interest; hence we call it a limit-deterministic Büchi supermartingale (LDBSM). Previously known supermartingale certificates applied only to quantitative reachability, safety, or reach-avoid properties, and to qualitative (i.e., probability 1) \r\n-regular properties.We also present fully automated algorithms for the template-based synthesis of LDBSMs, for the case when the stochastic system dynamics and the controller can be represented in terms of polynomial inequalities. Our experiments demonstrate the ability of our method to solve verification and control tasks for stochastic systems that were beyond the reach of previous supermartingale-based approaches.","lang":"eng"}],"intvolume":" 15932","has_accepted_license":"1","title":"Supermartingale certificates for quantitative omega-regular verification and control","publication_status":"published","volume":15932,"month":"07","scopus_import":"1","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031986789"],"eissn":["1611-3349"]},"oa":1,"arxiv":1,"acknowledgement":"This work was supported in part by the Singapore Ministry of Education (MOE) Academic Research Fund (AcRF) Tier 1 grant (Project ID:22-SIS-SMU-100) and the ERC project ERC-2020-AdG 101020093.","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik"},{"first_name":"Pouya","last_name":"Sadeghi","full_name":"Sadeghi, Pouya"},{"last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"page":"29-55","isi":1,"citation":{"ieee":"T. A. Henzinger, K. Mallik, P. Sadeghi, and D. Zikelic, “Supermartingale certificates for quantitative omega-regular verification and control,” in 37th International Conference on Computer Aided Verification, Zagreb, Croatia, 2025, vol. 15932, pp. 29–55.","mla":"Henzinger, Thomas A., et al. “Supermartingale Certificates for Quantitative Omega-Regular Verification and Control.” 37th International Conference on Computer Aided Verification, vol. 15932, Springer Nature, 2025, pp. 29–55, doi:10.1007/978-3-031-98679-6_2.","short":"T.A. Henzinger, K. Mallik, P. Sadeghi, D. Zikelic, in:, 37th International Conference on Computer Aided Verification, Springer Nature, 2025, pp. 29–55.","ista":"Henzinger TA, Mallik K, Sadeghi P, Zikelic D. 2025. Supermartingale certificates for quantitative omega-regular verification and control. 37th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 15932, 29–55.","chicago":"Henzinger, Thomas A, Kaushik Mallik, Pouya Sadeghi, and Dorde Zikelic. “Supermartingale Certificates for Quantitative Omega-Regular Verification and Control.” In 37th International Conference on Computer Aided Verification, 15932:29–55. Springer Nature, 2025. https://doi.org/10.1007/978-3-031-98679-6_2.","ama":"Henzinger TA, Mallik K, Sadeghi P, Zikelic D. Supermartingale certificates for quantitative omega-regular verification and control. In: 37th International Conference on Computer Aided Verification. Vol 15932. Springer Nature; 2025:29-55. doi:10.1007/978-3-031-98679-6_2","apa":"Henzinger, T. A., Mallik, K., Sadeghi, P., & Zikelic, D. (2025). Supermartingale certificates for quantitative omega-regular verification and control. In 37th International Conference on Computer Aided Verification (Vol. 15932, pp. 29–55). Zagreb, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-98679-6_2"},"article_processing_charge":"Yes (in subscription journal)"},{"oa":1,"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_created":"2025-08-31T15:14:18Z","keyword":["sustainability","conference travel"],"author":[{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"status":"public","citation":{"mla":"Schanda, Paul. Data of: “Quantifying the Carbon Footprint of Conference Travel: The Case of NMR Meetings.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20242.","ieee":"P. Schanda, “Data of: ‘Quantifying the carbon footprint of conference travel: the case of NMR meetings.’” Institute of Science and Technology Austria, 2025.","short":"P. Schanda, (2025).","apa":"Schanda, P. (2025). Data of: “Quantifying the carbon footprint of conference travel: the case of NMR meetings.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20242","ama":"Schanda P. Data of: “Quantifying the carbon footprint of conference travel: the case of NMR meetings.” 2025. doi:10.15479/AT-ISTA-20242","ista":"Schanda P. 2025. Data of: ‘Quantifying the carbon footprint of conference travel: the case of NMR meetings’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20242.","chicago":"Schanda, Paul. “Data of: ‘Quantifying the Carbon Footprint of Conference Travel: The Case of NMR Meetings.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20242."},"date_published":"2025-09-01T00:00:00Z","article_processing_charge":"No","contributor":[{"contributor_type":"researcher","last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"},{"first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","contributor_type":"researcher"},{"first_name":"Valentin","id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d","last_name":"Leitner","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Zivadinovic","first_name":"Predrag","id":"68AA0E5A-AFDA-11E9-9994-141DE6697425"},{"last_name":"Sisak","first_name":"Maria A","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Cecelia N","id":"2a69ab4b-896a-11ed-bdf8-cb8641cf2b21","last_name":"Mweka"},{"id":"c15a5412-de82-11ed-b809-8dc1aa996e40","first_name":"Jeroen A","last_name":"Dobbelaere","contributor_type":"supervisor"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","contributor_type":"supervisor"}],"year":"2025","month":"09","type":"research_data","publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"doi":"10.15479/AT-ISTA-20242","file_date_updated":"2025-09-01T11:05:27Z","abstract":[{"lang":"eng","text":"This repository contains calculations of carbon footprints of NMR conferences, as described in the article by \r\nLucky N. Kapoor, Natalia Ruzickova, Predrag Živadinović, Valentin Leitner, Maria Anna Sisak, Cecelia Mweka, Jeroen Dobbelaere, Georgios Katsaros, and Paul Schanda\r\nPublished in Magnetic Resonance, 2025."}],"oa_version":"Published Version","has_accepted_license":"1","_id":"20242","corr_author":"1","file":[{"creator":"pschanda","file_id":"20244","file_size":42368943,"file_name":"Abstracts.zip","checksum":"055044b03f835cb98c45d0504f1db96e","date_updated":"2025-08-31T15:09:44Z","access_level":"open_access","success":1,"content_type":"application/zip","date_created":"2025-08-31T15:09:44Z","relation":"main_file"},{"file_id":"20245","file_size":470659,"file_name":"data_CO2_conferences.zip","creator":"pschanda","date_updated":"2025-08-31T15:11:58Z","access_level":"open_access","checksum":"1492683af736ac65088b77e12b52c3b0","content_type":"application/zip","success":1,"date_created":"2025-08-31T15:11:58Z","relation":"main_file"},{"creator":"pschanda","file_id":"20246","file_size":1138772,"file_name":"Figure6_predictions.zip","checksum":"8ac69071f7508e77b5ca91fa5018339a","date_updated":"2025-08-31T15:12:03Z","access_level":"open_access","content_type":"application/zip","success":1,"date_created":"2025-08-31T15:12:03Z","relation":"main_file"},{"creator":"pschanda","file_size":6558,"file_name":"ExcelFileAnalysisCode.py","file_id":"20247","checksum":"19b77db247feecdc36fbe6f68d94a76d","access_level":"open_access","date_updated":"2025-08-31T15:12:07Z","date_created":"2025-08-31T15:12:07Z","success":1,"content_type":"text/x-python-script","relation":"main_file"},{"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2025-08-31T15:12:11Z","checksum":"39655e28c6df523f4f9662dc58c94623","date_updated":"2025-08-31T15:12:11Z","access_level":"open_access","creator":"pschanda","file_id":"20248","file_name":"emissions_spectrometers_and_Parisgoal.pdf","file_size":1107467},{"success":1,"content_type":"application/octet-stream","date_created":"2025-09-01T11:05:27Z","relation":"main_file","creator":"pschanda","file_id":"20263","file_name":"README","file_size":3994,"checksum":"2e9a9460b3f2abe7e46179561a63492b","date_updated":"2025-09-01T11:05:27Z","access_level":"open_access"}],"title":"Data of: \"Quantifying the carbon footprint of conference travel: the case of NMR meetings\"","department":[{"_id":"PaSc"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"20664"}]},"date_updated":"2026-06-10T08:45:12Z"},{"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"volume":542,"month":"09","scopus_import":"1","author":[{"full_name":"Sullivan, James","last_name":"Sullivan","first_name":"James"},{"last_name":"Haiman","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","orcid":"0000-0003-3633-5403","full_name":"Haiman, Zoltán"},{"full_name":"Kulkarni, Mihir","last_name":"Kulkarni","first_name":"Mihir"},{"full_name":"Visbal, Eli","last_name":"Visbal","first_name":"Eli"}],"language":[{"iso":"eng"}],"page":"822-838","citation":{"ama":"Sullivan J, Haiman Z, Kulkarni M, Visbal E. Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback? Monthly Notices of the Royal Astronomical Society. 2025;542(2):822-838. doi:10.1093/mnras/staf1269","apa":"Sullivan, J., Haiman, Z., Kulkarni, M., & Visbal, E. (2025). Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback? Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/staf1269","chicago":"Sullivan, James, Zoltán Haiman, Mihir Kulkarni, and Eli Visbal. “Can Supermassive Stars Form in Protogalaxies Due to Internal Lyman-Werner Feedback?” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2025. https://doi.org/10.1093/mnras/staf1269.","ista":"Sullivan J, Haiman Z, Kulkarni M, Visbal E. 2025. Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback? Monthly Notices of the Royal Astronomical Society. 542(2), 822–838.","short":"J. Sullivan, Z. Haiman, M. Kulkarni, E. Visbal, Monthly Notices of the Royal Astronomical Society 542 (2025) 822–838.","ieee":"J. Sullivan, Z. Haiman, M. Kulkarni, and E. Visbal, “Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback?,” Monthly Notices of the Royal Astronomical Society, vol. 542, no. 2. Oxford University Press, pp. 822–838, 2025.","mla":"Sullivan, James, et al. “Can Supermassive Stars Form in Protogalaxies Due to Internal Lyman-Werner Feedback?” Monthly Notices of the Royal Astronomical Society, vol. 542, no. 2, Oxford University Press, 2025, pp. 822–38, doi:10.1093/mnras/staf1269."},"article_processing_charge":"Yes","isi":1,"oa":1,"arxiv":1,"acknowledgement":"We thank the anonymous referee for comments that helped us improve the clarity of this manuscript. We acknowledge support from the United States National Science Foundation (NSF) grant AST-2006176 and the National Aeronautics and Space Administration (NASA) grants 80NSSC24K0440 and 80NSSC22K0822 (ZH). We also acknowledge support from NSF grant AST-2009309, NASA Astrophysics Theory Program grant 80NSSC22K0629, and Space Telescope Science Institute grant JWST-AR-05238 (EV). The simulations in this work were run on Texas Advanced Computing Center’s Stampede2 and Stampede3 systems. We used Stampede2 and Purdue University’s computing system Anvil for data analysis.","day":"01","quality_controlled":"1","publication":"Monthly Notices of the Royal Astronomical Society","OA_place":"publisher","abstract":[{"lang":"eng","text":"Population III stars are possible precursors to early supermassive black holes (BHs). The presence of soft UV Lyman–Werner (LW) background radiation can suppress Population III star formation in minihaloes and allow them to form in pristine atomic-cooling haloes. In the absence of molecular hydrogen (H2) cooling, atomic-cooling haloes enable rapid collapse with suppressed fragmentation. High background LW fluxes from preceding star-formation have been proposed to dissociate H2. This flux can be supplemented by LW radiation from one or more Population III star(s) in the same halo, reducing the necessary background level. Here, we consider atomic-cooling haloes in which multiple protostellar cores form close to one another nearly simultaneously. We assess whether the first star’s LW radiation can dissociate nearby \r\n, enabling rapid accretion on to a nearby protostellar core, and the prompt formation of a second, supermassive star (SMS) from warm, atomically-cooled gas. We use a set of hydrodynamical simulations with the code enzo, with identical LW backgrounds centred on a halo with two adjacent collapsing gas clumps. When an additional large local LW flux is introduced, we observe immediate reductions in both the accretion rates and the stellar masses that form within these clumps. While the LW flux reduces the H2 fraction and increases the gas temperature, the halo core’s potential well is too shallow to promptly heat the gas to >1000 K and increase the second protostar’s accretion rate. We conclude that this internal LW feedback scenario is unlikely to facilitate SMS or massive BH seed formation."}],"intvolume":" 542","has_accepted_license":"1","title":"Can supermassive stars form in protogalaxies due to internal Lyman-Werner feedback?","publication_status":"published","OA_type":"gold","article_type":"original","type":"journal_article","publisher":"Oxford University Press","ddc":["520"],"issue":"2","year":"2025","status":"public","date_published":"2025-09-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-08-31T22:01:31Z","external_id":{"arxiv":["2501.12986"],"isi":["001553472000001"]},"date_updated":"2025-09-30T14:28:05Z","department":[{"_id":"ZoHa"}],"file_date_updated":"2025-09-03T05:44:47Z","DOAJ_listed":"1","oa_version":"Published Version","file":[{"relation":"main_file","date_created":"2025-09-03T05:44:47Z","success":1,"content_type":"application/pdf","access_level":"open_access","date_updated":"2025-09-03T05:44:47Z","checksum":"2a06796b27da0b33d479dba170ba4b3f","file_name":"2025_MonthlyNoticesRAS_Sullivan.pdf","file_size":2780496,"file_id":"20279","creator":"dernst"}],"_id":"20250","PlanS_conform":"1","doi":"10.1093/mnras/staf1269","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"department":[{"_id":"RoSe"}],"date_updated":"2025-09-30T14:27:35Z","external_id":{"isi":["001558641300006"],"arxiv":["2410.20113"]},"doi":"10.1007/s00526-025-03062-x","_id":"20251","article_number":"226","oa_version":"Preprint","year":"2025","issue":"7","type":"journal_article","article_type":"original","publisher":"Springer Nature","date_created":"2025-08-31T22:01:31Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","date_published":"2025-09-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2410.20113"}],"quality_controlled":"1","day":"01","OA_type":"green","publication_status":"published","title":"Stability estimate for the Lane–Emden inequality","OA_place":"repository","publication":"Calculus of Variations and Partial Differential Equations","abstract":[{"lang":"eng","text":"The Lane–Emden inequality controls (math. formular) in terms of the L^1 and L^p norms of p. We provide a remainder estimate for this inequality in terms of a suitable distance of p to the manifold of optimizers."}],"intvolume":" 64","volume":64,"month":"09","scopus_import":"1","publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"arxiv":1,"acknowledgement":"We are grateful to Rupert Frank and Enno Lenzmann for helpful discussions.","oa":1,"article_processing_charge":"No","isi":1,"citation":{"ieee":"E. Carlen, M. Lewin, E. H. Lieb, and R. Seiringer, “Stability estimate for the Lane–Emden inequality,” Calculus of Variations and Partial Differential Equations, vol. 64, no. 7. Springer Nature, 2025.","mla":"Carlen, Eric, et al. “Stability Estimate for the Lane–Emden Inequality.” Calculus of Variations and Partial Differential Equations, vol. 64, no. 7, 226, Springer Nature, 2025, doi:10.1007/s00526-025-03062-x.","short":"E. Carlen, M. Lewin, E.H. Lieb, R. Seiringer, Calculus of Variations and Partial Differential Equations 64 (2025).","ama":"Carlen E, Lewin M, Lieb EH, Seiringer R. Stability estimate for the Lane–Emden inequality. Calculus of Variations and Partial Differential Equations. 2025;64(7). doi:10.1007/s00526-025-03062-x","apa":"Carlen, E., Lewin, M., Lieb, E. H., & Seiringer, R. (2025). Stability estimate for the Lane–Emden inequality. Calculus of Variations and Partial Differential Equations. Springer Nature. https://doi.org/10.1007/s00526-025-03062-x","ista":"Carlen E, Lewin M, Lieb EH, Seiringer R. 2025. Stability estimate for the Lane–Emden inequality. Calculus of Variations and Partial Differential Equations. 64(7), 226.","chicago":"Carlen, Eric, Mathieu Lewin, Elliott H. Lieb, and Robert Seiringer. “Stability Estimate for the Lane–Emden Inequality.” Calculus of Variations and Partial Differential Equations. Springer Nature, 2025. https://doi.org/10.1007/s00526-025-03062-x."},"author":[{"full_name":"Carlen, Eric","first_name":"Eric","last_name":"Carlen"},{"full_name":"Lewin, Mathieu","first_name":"Mathieu","last_name":"Lewin"},{"full_name":"Lieb, Elliott H.","first_name":"Elliott H.","last_name":"Lieb"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"language":[{"iso":"eng"}]},{"OA_type":"green","abstract":[{"lang":"eng","text":"Zirconia nanocrystals (ZrO2 NCs) are a stable host material for lanthanides, but their performance lags behind that of the leading NaYF4 nanomaterials. Here, we leverage surface chemistry and core/shell architectures to uncover the contribution of dopants at the nanocrystal surface and of dopants in the nanocrystal bulk. We first assess the doping efficiency by ICP and find that, while Eu is almost quantitatively incorporated, the other lanthanides (La, Ce, Tb, Tm, Er, Yb) have about 50% incorporation efficiency over the studied doping range of 1–10%. We then determine the nanocrystal surface chemistry using NMR spectroscopy, despite the additional spectral line broadening caused by the paramagnetic lanthanide dopants. By varying the surface ligands and measuring the photoluminescence, we resolve the spectroscopic signals that are sensitive to a change in surface chemistry. Time-resolved emission spectra further reinforce the notion of a bulk component with a long luminescent lifetime and a surface component with a fast lifetime. Upon shelling Eu- or Tb-doped zirconia NCs with pure zirconia, the surface component disappears, and the photoluminescence quantum yield increases. We further functionalized the surface of the core/shell particles with oleylphosphonic acid ligands to obtain excellent dispersibility. These results show that lanthanide-doped zirconia NCs can be engineered to eliminate deactivation pathways."}],"intvolume":" 19","publication":"ACS Nano","OA_place":"repository","publication_status":"published","title":"Identification and elimination of surface emission in lanthanide (Co)doped zirconia nanocrystals","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2025-r1gw4"}],"day":"26","quality_controlled":"1","oa":1,"acknowledgement":"N.R. and C.S. thank the SNSF Eccellenza funding scheme (Project 194172) for funding. D.V.d.H. is supported by the Research Foundation Flanders (FWO) through a Senior Postdoctoral Research Fellowship (N° 1237825N). P.F.S. acknowledges the Special Research Fund at UGent (bof/baf/4y/2024/01/037). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by the electron microscopy facility (EMF). We thank Tommaso Costanzo for providing assistance during STEM measurements. We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz Association HGF, for the provision of experimental facilities. Parts of this research were carried out using beamline P21.1 at PETRA III, and the authors thank Ann-Christin Dippel, Jiatu Liu, and Fernando Igoa for assistance in using the beamline for PDF acquisition (Proposal I-20231114 EC). The authors thank Daniel Häussinger for help with the analysis of NMR spectra.","language":[{"iso":"eng"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"author":[{"first_name":"Nico","last_name":"Reichholf","full_name":"Reichholf, Nico"},{"last_name":"Horta","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona"},{"full_name":"Van Der Heggen, David","first_name":"David","last_name":"Van Der Heggen"},{"full_name":"Seno, Carlotta","first_name":"Carlotta","last_name":"Seno"},{"full_name":"Pulparayil Mathew, Jikson","first_name":"Jikson","last_name":"Pulparayil Mathew"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Smet, Philippe F.","first_name":"Philippe F.","last_name":"Smet"},{"full_name":"De Roo, Jonathan","first_name":"Jonathan","last_name":"De Roo"}],"citation":{"ieee":"N. Reichholf et al., “Identification and elimination of surface emission in lanthanide (Co)doped zirconia nanocrystals,” ACS Nano, vol. 19, no. 33. American Chemical Society, pp. 30371–30382, 2025.","mla":"Reichholf, Nico, et al. “Identification and Elimination of Surface Emission in Lanthanide (Co)Doped Zirconia Nanocrystals.” ACS Nano, vol. 19, no. 33, American Chemical Society, 2025, pp. 30371–82, doi:10.1021/acsnano.5c09137.","short":"N. Reichholf, S. Horta, D. Van Der Heggen, C. Seno, J. Pulparayil Mathew, M. Ibáñez, P.F. Smet, J. De Roo, ACS Nano 19 (2025) 30371–30382.","chicago":"Reichholf, Nico, Sharona Horta, David Van Der Heggen, Carlotta Seno, Jikson Pulparayil Mathew, Maria Ibáñez, Philippe F. Smet, and Jonathan De Roo. “Identification and Elimination of Surface Emission in Lanthanide (Co)Doped Zirconia Nanocrystals.” ACS Nano. American Chemical Society, 2025. https://doi.org/10.1021/acsnano.5c09137.","ista":"Reichholf N, Horta S, Van Der Heggen D, Seno C, Pulparayil Mathew J, Ibáñez M, Smet PF, De Roo J. 2025. Identification and elimination of surface emission in lanthanide (Co)doped zirconia nanocrystals. ACS Nano. 19(33), 30371–30382.","ama":"Reichholf N, Horta S, Van Der Heggen D, et al. Identification and elimination of surface emission in lanthanide (Co)doped zirconia nanocrystals. ACS Nano. 2025;19(33):30371-30382. doi:10.1021/acsnano.5c09137","apa":"Reichholf, N., Horta, S., Van Der Heggen, D., Seno, C., Pulparayil Mathew, J., Ibáñez, M., … De Roo, J. (2025). Identification and elimination of surface emission in lanthanide (Co)doped zirconia nanocrystals. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.5c09137"},"article_processing_charge":"No","isi":1,"page":"30371-30382","scopus_import":"1","month":"08","volume":19,"publication_identifier":{"eissn":["1936-086X"]},"doi":"10.1021/acsnano.5c09137","oa_version":"Preprint","_id":"20252","department":[{"_id":"MaIb"}],"external_id":{"isi":["001550173000001"]},"date_updated":"2025-09-30T14:27:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-08-31T22:01:31Z","date_published":"2025-08-26T00:00:00Z","status":"public","acknowledged_ssus":[{"_id":"EM-Fac"}],"issue":"33","year":"2025","publisher":"American Chemical Society","type":"journal_article","article_type":"original"},{"has_accepted_license":"1","publication_status":"published","corr_author":"1","title":"Quantitative language automata","publication":"36th International Conference on Concurrency Theory","OA_place":"publisher","intvolume":" 348","abstract":[{"lang":"eng","text":"A quantitative word automaton (QWA) defines a function from infinite words to values. For example, every infinite run of a limit-average QWA 𝒜 obtains a mean payoff, and every word w ∈ Σ^ω is assigned the maximal mean payoff obtained by nondeterministic runs of 𝒜 over w. We introduce quantitative language automata (QLAs) that define functions from language generators (i.e., implementations) to values, where a language generator can be nonprobabilistic, defining a set of infinite words, or probabilistic, defining a probability measure over infinite words. A QLA consists of a QWA and an aggregator function. For example, given a QWA 𝒜, the infimum aggregator maps each language L ⊆ Σ^ω to the greatest lower bound assigned by 𝒜 to any word in L. For boolean value sets, QWAs define boolean properties of traces, and QLAs define boolean properties of sets of traces, i.e., hyperproperties. For more general value sets, QLAs serve as a specification language for a generalization of hyperproperties, called quantitative hyperproperties. A nonprobabilistic (resp. probabilistic) quantitative hyperproperty assigns a value to each set (resp. distribution) G of traces, e.g., the minimal (resp. expected) average response time exhibited by the traces in G. We give several examples of quantitative hyperproperties and investigate three paradigmatic problems for QLAs: evaluation, nonemptiness, and universality. In the evaluation problem, given a QLA 𝔸 and an implementation G, we ask for the value that 𝔸 assigns to G. In the nonemptiness (resp. universality) problem, given a QLA 𝔸 and a value k, we ask whether 𝔸 assigns at least k to some (resp. every) language. We provide a comprehensive picture of decidability for these problems for QLAs with common aggregators as well as their restrictions to ω-regular languages and trace distributions generated by finite-state Markov chains."}],"OA_type":"gold","ec_funded":1,"quality_controlled":"1","day":"18","isi":1,"citation":{"mla":"Henzinger, Thomas A., et al. “Quantitative Language Automata.” 36th International Conference on Concurrency Theory, vol. 348, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, doi:10.4230/LIPIcs.CONCUR.2025.21.","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Quantitative language automata,” in 36th International Conference on Concurrency Theory, Aarhus, Denmark, 2025, vol. 348.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2025). Quantitative language automata. In 36th International Conference on Concurrency Theory (Vol. 348). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2025.21","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Quantitative language automata. In: 36th International Conference on Concurrency Theory. Vol 348. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025. doi:10.4230/LIPIcs.CONCUR.2025.21","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2025. Quantitative language automata. 36th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 348, 21.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Language Automata.” In 36th International Conference on Concurrency Theory, Vol. 348. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. https://doi.org/10.4230/LIPIcs.CONCUR.2025.21.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 36th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025."},"article_processing_charge":"No","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"full_name":"Kebis, Pavol","first_name":"Pavol","id":"2e0132b3-4e98-11ef-b275-cf7281c2802a","last_name":"Kebis"},{"last_name":"Mazzocchi","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","full_name":"Mazzocchi, Nicolas Adrien"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac"}],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"arxiv":1,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.","oa":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773898"]},"volume":348,"scopus_import":"1","month":"08","alternative_title":["LIPIcs"],"_id":"20253","article_number":"21","file":[{"checksum":"9d4054058757a73477e6015b10ed6996","access_level":"open_access","date_updated":"2025-09-03T10:01:53Z","creator":"dernst","file_name":"2025_CONCUR_HenzingerT.pdf","file_size":1257397,"file_id":"20282","relation":"main_file","date_created":"2025-09-03T10:01:53Z","content_type":"application/pdf","success":1}],"file_date_updated":"2025-09-03T10:01:53Z","oa_version":"Published Version","doi":"10.4230/LIPIcs.CONCUR.2025.21","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-12-01T12:36:52Z","external_id":{"isi":["001570540800021"],"arxiv":["2506.0515"]},"department":[{"_id":"ToHe"}],"status":"public","date_published":"2025-08-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-31T22:01:32Z","type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"start_date":"2025-08-26","name":"CONCUR: Conference on Concurrency Theory","end_date":"2025-08-29","location":"Aarhus, Denmark"},"year":"2025","ddc":["000"]},{"year":"2025","issue":"8","ddc":["000"],"publisher":"Oxford University Press","article_type":"original","type":"journal_article","date_created":"2025-08-31T22:01:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2025-08-01T00:00:00Z","status":"public","department":[{"_id":"KrCh"}],"APC_amount":"4493,27 EUR","date_updated":"2026-06-11T09:11:17Z","external_id":{"arxiv":["2503.09841"]},"doi":"10.1093/pnasnexus/pgaf252","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"PlanS_conform":"1","_id":"20254","file":[{"date_updated":"2025-09-03T06:20:08Z","access_level":"open_access","checksum":"8a5e82c6f842e3220ec96028c9374b69","file_id":"20280","file_size":1086419,"file_name":"2025_PNASNexus_Brewster.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2025-09-03T06:20:08Z"}],"article_number":"pgaf252","oa_version":"Published Version","file_date_updated":"2025-09-03T06:20:08Z","DOAJ_listed":"1","scopus_import":"1","month":"08","volume":4,"publication_identifier":{"eissn":["2752-6542"]},"acknowledgement":"J.S. and K.C. were supported by the European Research Council CoG 863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12. J.T. was supported by GAČR grant 25-17377S and by Charles Univ. projects UNCE 24/SCI/008 and PRIMUS 24/SCI/012.","arxiv":1,"oa":1,"citation":{"mla":"Brewster, David A., et al. “Maintaining Diversity in Structured Populations.” PNAS Nexus, vol. 4, no. 8, pgaf252, Oxford University Press, 2025, doi:10.1093/pnasnexus/pgaf252.","ieee":"D. A. Brewster, J. Svoboda, D. Roscow, K. Chatterjee, J. Tkadlec, and M. A. Nowak, “Maintaining diversity in structured populations,” PNAS Nexus, vol. 4, no. 8. Oxford University Press, 2025.","chicago":"Brewster, David A., Jakub Svoboda, Dylan Roscow, Krishnendu Chatterjee, Josef Tkadlec, and Martin A. Nowak. “Maintaining Diversity in Structured Populations.” PNAS Nexus. Oxford University Press, 2025. https://doi.org/10.1093/pnasnexus/pgaf252.","ista":"Brewster DA, Svoboda J, Roscow D, Chatterjee K, Tkadlec J, Nowak MA. 2025. Maintaining diversity in structured populations. PNAS Nexus. 4(8), pgaf252.","ama":"Brewster DA, Svoboda J, Roscow D, Chatterjee K, Tkadlec J, Nowak MA. Maintaining diversity in structured populations. PNAS Nexus. 2025;4(8). doi:10.1093/pnasnexus/pgaf252","apa":"Brewster, D. A., Svoboda, J., Roscow, D., Chatterjee, K., Tkadlec, J., & Nowak, M. A. (2025). Maintaining diversity in structured populations. PNAS Nexus. Oxford University Press. https://doi.org/10.1093/pnasnexus/pgaf252","short":"D.A. Brewster, J. Svoboda, D. Roscow, K. Chatterjee, J. Tkadlec, M.A. Nowak, PNAS Nexus 4 (2025)."},"article_processing_charge":"Yes","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"language":[{"iso":"eng"}],"author":[{"first_name":"David A.","last_name":"Brewster","full_name":"Brewster, David A."},{"first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"},{"full_name":"Roscow, Dylan","first_name":"Dylan","last_name":"Roscow"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"quality_controlled":"1","day":"01","OA_type":"gold","ec_funded":1,"title":"Maintaining diversity in structured populations","publication_status":"published","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We examine population structures for their ability to maintain diversity in neutral evolution. We use the general framework of evolutionary graph theory and consider birth–death (bd) and death–birth (db) updating. The population is of size N. Initially all individuals represent different types. The basic question is: what is the time TN until one type takes over the population? This time is known as consensus time in computer science and as total coalescent time in evolutionary biology. For the complete graph, it is known that TN is quadratic in N for db and bd. For the cycle, we prove that TN is cubic in N for db and bd. For the star, we prove that TN is cubic for bd and quasilinear (N log N) for db. For the double star, we show that TN is quartic for bd. We derive upper and lower bounds for all undirected graphs for bd and db. We also show the Pareto front of graphs (of size N = 8) that maintain diversity the longest for bd and db. Further, we show that some graphs that quickly homogenize can maintain high levels of diversity longer than graphs that slowly homogenize. For directed graphs, we give simple contracting star-like structures that have superexponential time scales for maintaining diversity."}],"intvolume":" 4","publication":"PNAS Nexus","OA_place":"publisher"},{"title":"The first billion years according to JWST","publication_status":"published","intvolume":" 9","abstract":[{"lang":"eng","text":"With stunning clarity, the JWST has revealed the Universe’s first billion years. The scientific community is analysing a wealth of JWST imaging and spectroscopic data from that era, and is in the process of rewriting the astronomy textbooks. Here, as a result of the 2024 ISSI Breakthrough Workshop, we provide a snapshot of the great progress made towards understanding the initial chapters of our cosmic history 1.5 years into the JWST science mission. We present the current census of early galaxies, their luminosities, appearance, chemical composition, masses and formation histories as revealed by JWST. We relate the discovery of massive black holes in early galaxies and discuss their demographics and implications for their formations and growth. We conclude by describing the potential sources of reionization and our current understanding of how the Universe became fully ionized. Throughout the Perspective, we highlight discoveries and breakthroughs, topics and issues that are not yet understood, and questions that will be addressed in the coming years, as JWST continues its revolutionary observations of the early Universe."}],"publication":"Nature Astronomy","OA_place":"repository","OA_type":"green","quality_controlled":"1","day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.21054"}],"isi":1,"citation":{"short":"A. Adamo, H. Atek, M.B. Bagley, E. Bañados, K.S.S. Barrow, D.A. Berg, R. Bezanson, M. Bradač, G. Brammer, A.C. Carnall, J. Chisholm, D. Coe, P. Dayal, D.J. Eisenstein, J.J. Eldridge, A. Ferrara, S. Fujimoto, A.D. Graaff, M. Habouzit, T.A. Hutchison, J.S. Kartaltepe, S.A. Kassin, M. Kriek, I. Labbé, R. Maiolino, R. Marques-Chaves, M.V. Maseda, C. Mason, J.J. Matthee, K.B.W. Mcquinn, G. Meynet, R.P. Naidu, P.A. Oesch, L. Pentericci, P.G. Pérez-González, J.R. Rigby, G. Roberts-Borsani, D. Schaerer, A.E. Shapley, D.P. Stark, M. Stiavelli, A.L. Strom, E. Vanzella, F. Wang, S.M. Wilkins, C.C. Williams, C.J. Willott, D. Wylezalek, A. Nota, Nature Astronomy 9 (2025) 1134–1147.","chicago":"Adamo, Angela, Hakim Atek, Micaela B. Bagley, Eduardo Bañados, Kirk S.S. Barrow, Danielle A. Berg, Rachel Bezanson, et al. “The First Billion Years According to JWST.” Nature Astronomy. Springer Nature, 2025. https://doi.org/10.1038/s41550-025-02624-5.","ista":"Adamo A, Atek H, Bagley MB, Bañados E, Barrow KSS, Berg DA, Bezanson R, Bradač M, Brammer G, Carnall AC, Chisholm J, Coe D, Dayal P, Eisenstein DJ, Eldridge JJ, Ferrara A, Fujimoto S, Graaff AD, Habouzit M, Hutchison TA, Kartaltepe JS, Kassin SA, Kriek M, Labbé I, Maiolino R, Marques-Chaves R, Maseda MV, Mason C, Matthee JJ, Mcquinn KBW, Meynet G, Naidu RP, Oesch PA, Pentericci L, Pérez-González PG, Rigby JR, Roberts-Borsani G, Schaerer D, Shapley AE, Stark DP, Stiavelli M, Strom AL, Vanzella E, Wang F, Wilkins SM, Williams CC, Willott CJ, Wylezalek D, Nota A. 2025. The first billion years according to JWST. Nature Astronomy. 9(8), 1134–1147.","apa":"Adamo, A., Atek, H., Bagley, M. B., Bañados, E., Barrow, K. S. S., Berg, D. A., … Nota, A. (2025). The first billion years according to JWST. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-025-02624-5","ama":"Adamo A, Atek H, Bagley MB, et al. The first billion years according to JWST. Nature Astronomy. 2025;9(8):1134-1147. doi:10.1038/s41550-025-02624-5","ieee":"A. Adamo et al., “The first billion years according to JWST,” Nature Astronomy, vol. 9, no. 8. Springer Nature, pp. 1134–1147, 2025.","mla":"Adamo, Angela, et al. “The First Billion Years According to JWST.” Nature Astronomy, vol. 9, no. 8, Springer Nature, 2025, pp. 1134–47, doi:10.1038/s41550-025-02624-5."},"article_processing_charge":"No","page":"1134-1147","language":[{"iso":"eng"}],"author":[{"first_name":"Angela","last_name":"Adamo","full_name":"Adamo, Angela"},{"full_name":"Atek, Hakim","last_name":"Atek","first_name":"Hakim"},{"first_name":"Micaela B.","last_name":"Bagley","full_name":"Bagley, Micaela B."},{"full_name":"Bañados, Eduardo","first_name":"Eduardo","last_name":"Bañados"},{"full_name":"Barrow, Kirk S.S.","first_name":"Kirk S.S.","last_name":"Barrow"},{"full_name":"Berg, Danielle A.","first_name":"Danielle A.","last_name":"Berg"},{"last_name":"Bezanson","first_name":"Rachel","full_name":"Bezanson, Rachel"},{"last_name":"Bradač","first_name":"Maruša","full_name":"Bradač, Maruša"},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"first_name":"Adam C.","last_name":"Carnall","full_name":"Carnall, Adam C."},{"full_name":"Chisholm, John","first_name":"John","last_name":"Chisholm"},{"first_name":"Dan","last_name":"Coe","full_name":"Coe, Dan"},{"full_name":"Dayal, Pratika","last_name":"Dayal","first_name":"Pratika"},{"last_name":"Eisenstein","first_name":"Daniel J.","full_name":"Eisenstein, Daniel J."},{"first_name":"Jan J.","last_name":"Eldridge","full_name":"Eldridge, Jan J."},{"full_name":"Ferrara, Andrea","first_name":"Andrea","last_name":"Ferrara"},{"last_name":"Fujimoto","first_name":"Seiji","full_name":"Fujimoto, Seiji"},{"last_name":"Graaff","first_name":"Anna De","full_name":"Graaff, Anna De"},{"full_name":"Habouzit, Melanie","first_name":"Melanie","last_name":"Habouzit"},{"full_name":"Hutchison, Taylor A.","first_name":"Taylor A.","last_name":"Hutchison"},{"full_name":"Kartaltepe, Jeyhan S.","first_name":"Jeyhan S.","last_name":"Kartaltepe"},{"first_name":"Susan A.","last_name":"Kassin","full_name":"Kassin, Susan A."},{"first_name":"Mariska","last_name":"Kriek","full_name":"Kriek, Mariska"},{"full_name":"Labbé, Ivo","last_name":"Labbé","first_name":"Ivo"},{"full_name":"Maiolino, Roberto","last_name":"Maiolino","first_name":"Roberto"},{"full_name":"Marques-Chaves, Rui","first_name":"Rui","last_name":"Marques-Chaves"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"last_name":"Mason","first_name":"Charlotte","full_name":"Mason, Charlotte"},{"orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Mcquinn, Kristen B.W.","last_name":"Mcquinn","first_name":"Kristen B.W."},{"full_name":"Meynet, Georges","last_name":"Meynet","first_name":"Georges"},{"full_name":"Naidu, Rohan P.","first_name":"Rohan P.","last_name":"Naidu"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"last_name":"Pentericci","first_name":"Laura","full_name":"Pentericci, Laura"},{"first_name":"Pablo G.","last_name":"Pérez-González","full_name":"Pérez-González, Pablo G."},{"full_name":"Rigby, Jane R.","first_name":"Jane R.","last_name":"Rigby"},{"first_name":"Guido","last_name":"Roberts-Borsani","full_name":"Roberts-Borsani, Guido"},{"full_name":"Schaerer, Daniel","last_name":"Schaerer","first_name":"Daniel"},{"last_name":"Shapley","first_name":"Alice E.","full_name":"Shapley, Alice E."},{"last_name":"Stark","first_name":"Daniel P.","full_name":"Stark, Daniel P."},{"first_name":"Massimo","last_name":"Stiavelli","full_name":"Stiavelli, Massimo"},{"last_name":"Strom","first_name":"Allison L.","full_name":"Strom, Allison L."},{"last_name":"Vanzella","first_name":"Eros","full_name":"Vanzella, Eros"},{"first_name":"Feige","last_name":"Wang","full_name":"Wang, Feige"},{"full_name":"Wilkins, Stephen M.","first_name":"Stephen M.","last_name":"Wilkins"},{"full_name":"Williams, Christina C.","last_name":"Williams","first_name":"Christina C."},{"full_name":"Willott, Chris J.","first_name":"Chris J.","last_name":"Willott"},{"full_name":"Wylezalek, Dominika","last_name":"Wylezalek","first_name":"Dominika"},{"full_name":"Nota, Antonella","first_name":"Antonella","last_name":"Nota"}],"acknowledgement":"While this Perspective is written by a small number of authors, invited to ISSI Bern in March 2024 as part of the 2024 ISSI Breakthrough Workshop, we acknowledge the work of a large community that is advancing our collective understanding of the evolution of the early Universe. We thank ISSI for sponsoring the 2024 Breakthrough Workshop, and the ISSI staff for their wonderful welcome and support. We are grateful to the author collaborators, who made this paper possible. Collectively, we are grateful to the large group of committed scientists and engineers, worldwide, who designed, built and commissioned the JWST and made a decades-long astronomer dream a reality. R.P.N. is a NASA Hubble Fellow. We are grateful to M. Dickinson for a careful read of the final paper and to F. Crameri (ISSI) for his expert help designing the very best figures. We dedicate this paper to the 20,000 people who spent decades to make JWST an incredible discovery machine.","arxiv":1,"oa":1,"publication_identifier":{"eissn":["2397-3366"]},"scopus_import":"1","month":"08","volume":9,"_id":"20255","oa_version":"Preprint","doi":"10.1038/s41550-025-02624-5","date_updated":"2025-09-30T14:28:42Z","external_id":{"arxiv":["2405.21054"],"isi":["001547681400001"]},"department":[{"_id":"JoMa"}],"date_published":"2025-08-01T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-08-31T22:01:32Z","publisher":"Springer Nature","type":"journal_article","article_type":"original","year":"2025","issue":"8"},{"file":[{"date_created":"2025-09-03T10:32:12Z","success":1,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_size":489639,"file_name":"2025_L4DC_HenzingerT.pdf","file_id":"20283","checksum":"d5236e561560635f5ae1d17de4903033","access_level":"open_access","date_updated":"2025-09-03T10:32:12Z"}],"_id":"20256","alternative_title":["PMLR"],"oa_version":"Published Version","file_date_updated":"2025-09-03T10:32:12Z","date_updated":"2025-09-03T10:37:59Z","external_id":{"arxiv":["2412.16564"]},"department":[{"_id":"ToHe"},{"_id":"ChLa"}],"date_published":"2025-06-01T00:00:00Z","status":"public","date_created":"2025-08-31T22:01:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","type":"conference","year":"2025","conference":{"name":"L4DC: Learning for Dynamics & Control","start_date":"2025-06-04","end_date":"2025-06-06","location":"Ann Arbor, MI, United States"},"ddc":["000"],"publication_status":"published","title":"Predictive monitoring of black-box dynamical systems","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"We study the problem of predictive runtime monitoring of black-box dynamical systems with quantitative safety properties. The black-box setting stipulates that the exact semantics of the dynamical system and the controller are unknown, and that we are only able to observe the state of the controlled (aka, closed-loop) system at finitely many time points. We present a novel framework for predicting future states of the system based on the states observed in the past. The numbers of past states and of predicted future states are parameters provided by the user. Our method is based on a combination of Taylor’s expansion and the backward difference operator for numerical differentiation. We also derive an upper bound on the prediction error under the assumption that the system dynamics and the controller are smooth. The predicted states are then used to predict safety violations ahead in time. Our experiments demonstrate practical applicability of our method for complex black-box systems, showing that it is computationally lightweight and yet significantly more accurate than the state-of-the-art predictive safety monitoring techniques.","lang":"eng"}],"intvolume":" 283","OA_place":"publisher","publication":"7th Annual Learning for Dynamics & Control Conference","OA_type":"gold","ec_funded":1,"quality_controlled":"1","day":"01","citation":{"ieee":"T. A. Henzinger, F. Kresse, K. Mallik, E. Yu, and D. Zikelic, “Predictive monitoring of black-box dynamical systems,” in 7th Annual Learning for Dynamics & Control Conference, Ann Arbor, MI, United States, 2025, vol. 283, pp. 804–816.","mla":"Henzinger, Thomas A., et al. “Predictive Monitoring of Black-Box Dynamical Systems.” 7th Annual Learning for Dynamics & Control Conference, vol. 283, ML Research Press, 2025, pp. 804–16.","apa":"Henzinger, T. A., Kresse, F., Mallik, K., Yu, E., & Zikelic, D. (2025). Predictive monitoring of black-box dynamical systems. In 7th Annual Learning for Dynamics & Control Conference (Vol. 283, pp. 804–816). Ann Arbor, MI, United States: ML Research Press.","ama":"Henzinger TA, Kresse F, Mallik K, Yu E, Zikelic D. Predictive monitoring of black-box dynamical systems. In: 7th Annual Learning for Dynamics & Control Conference. Vol 283. ML Research Press; 2025:804-816.","ista":"Henzinger TA, Kresse F, Mallik K, Yu E, Zikelic D. 2025. Predictive monitoring of black-box dynamical systems. 7th Annual Learning for Dynamics & Control Conference. L4DC: Learning for Dynamics & Control, PMLR, vol. 283, 804–816.","chicago":"Henzinger, Thomas A, Fabian Kresse, Kaushik Mallik, Emily Yu, and Dorde Zikelic. “Predictive Monitoring of Black-Box Dynamical Systems.” In 7th Annual Learning for Dynamics & Control Conference, 283:804–16. ML Research Press, 2025.","short":"T.A. Henzinger, F. Kresse, K. Mallik, E. Yu, D. Zikelic, in:, 7th Annual Learning for Dynamics & Control Conference, ML Research Press, 2025, pp. 804–816."},"article_processing_charge":"No","page":"804-816","language":[{"iso":"eng"}],"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"author":[{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"first_name":"Fabian","id":"faff3c84-23f6-11ef-9085-e5187b51c604","last_name":"Kresse","full_name":"Kresse, Fabian"},{"orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik"},{"full_name":"Yu, Zhengqi","first_name":"Zhengqi","id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342","last_name":"Yu"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699"}],"acknowledgement":"This work was supported in part by the ERC project ERC-2020-AdG 101020093.\r\n","arxiv":1,"oa":1,"publication_identifier":{"eissn":["2640-3498"]},"month":"06","scopus_import":"1","volume":283},{"quality_controlled":"1","day":"01","OA_type":"hybrid","has_accepted_license":"1","corr_author":"1","publication_status":"published","title":"Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme","publication":"Journal of Molecular Biology","OA_place":"publisher","abstract":[{"text":"The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR.","lang":"eng"}],"intvolume":" 437","volume":437,"month":"12","scopus_import":"1","publication_identifier":{"issn":["0022-2836"],"eissn":["1089-8638"]},"acknowledgement":"This work was supported financially by the Austrian Science Fund (FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent support of the NMR facility.","oa":1,"article_processing_charge":"Yes (via OA deal)","citation":{"ista":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 437(23), 169379.","chicago":"Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Journal of Molecular Biology. Elsevier, 2025. https://doi.org/10.1016/j.jmb.2025.169379.","ama":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169379","apa":"Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., & Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2025.169379","short":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda, Journal of Molecular Biology 437 (2025).","mla":"Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Journal of Molecular Biology, vol. 437, no. 23, 169379, Elsevier, 2025, doi:10.1016/j.jmb.2025.169379.","ieee":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P. Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme,” Journal of Molecular Biology, vol. 437, no. 23. Elsevier, 2025."},"isi":1,"author":[{"full_name":"Rohden, Darja","first_name":"Darja","id":"81dc668a-19fa-11f0-bf31-d56534059ef3","last_name":"Rohden"},{"orcid":"0000-0002-9043-136X","full_name":"Napoli, Federico","last_name":"Napoli","first_name":"Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b"},{"first_name":"Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova","full_name":"Kapitonova, Anna"},{"full_name":"Tatman, Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f","first_name":"Benjamin","last_name":"Tatman"},{"last_name":"Lichtenecker","first_name":"Roman J.","full_name":"Lichtenecker, Roman J."},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"}],"department":[{"_id":"PaSc"}],"related_material":{"record":[{"id":"19956","relation":"research_data","status":"public"}]},"date_updated":"2026-06-10T08:20:37Z","external_id":{"isi":["001618289100020"]},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.jmb.2025.169379","PlanS_conform":"1","file":[{"file_size":2270555,"file_name":"2025_JourMolecularBiology_Rohden.pdf","file_id":"20876","creator":"dernst","access_level":"open_access","date_updated":"2025-12-29T14:51:40Z","checksum":"90d50594d8ea9860ac5da41297992847","date_created":"2025-12-29T14:51:40Z","success":1,"content_type":"application/pdf","relation":"main_file"}],"_id":"20258","article_number":"169379","file_date_updated":"2025-12-29T14:51:40Z","oa_version":"Published Version","year":"2025","ddc":["540"],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"issue":"23","type":"journal_article","article_type":"original","publisher":"Elsevier","date_created":"2025-08-31T22:01:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2025-12-01T00:00:00Z"},{"department":[{"_id":"EdHa"}],"date_updated":"2025-12-30T09:34:11Z","external_id":{"isi":["001556019400001"]},"doi":"10.1038/s41567-025-02980-z","_id":"20259","oa_version":"None","year":"2025","type":"journal_article","article_type":"original","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-31T22:01:33Z","status":"public","date_published":"2025-09-01T00:00:00Z","quality_controlled":"1","day":"01","OA_type":"closed access","corr_author":"1","publication_status":"published","title":"The actin cortex acts as a mechanical memory of morphology in confined migrating cells","publication":"Nature Physics","abstract":[{"text":"Cell migration in narrow microenvironments occurs in numerous physiological processes. It involves successive cycles of confinement and release that drive important morphological changes. However, it remains unclear whether migrating cells can retain a memory of their past morphological states that could potentially facilitate their navigation through confined spaces. We demonstrate that local geometry governs a switch between two cell morphologies, thereby facilitating cell passage through long and narrow gaps. We combined cell migration assays on standardized microsystems with biophysical modelling and biochemical perturbations to show that migrating cells have a long-term memory of past confinement events. The morphological cell states correlate across transitions through actin cortex remodelling. These findings indicate that mechanical memory in migrating cells plays an active role in their migratory potential in confined environments.","lang":"eng"}],"intvolume":" 21","volume":21,"scopus_import":"1","month":"09","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"acknowledgement":"We are grateful to members of S.G.’s laboratory for feedback and suggestions. We thank E. Hannezo, J. O. Rädler, M. Piel, O. du Roure and J. Heuvingh for inspiring discussions. Y.K. and S.G. acknowledge J. B. Braquenier from Nikon Instruments Belux and the Nikon BioImaging Lab in Leiden (the Netherlands) for their support with the Nikon Spatial Array Confocal enhanced-resolution confocal microscopy. We thank D. S. Herrador and M. Balland for their help in improving the microprinting method. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). Y.K., M.L. and S.G. acknowledge funding from the University of Mons (FEDER Prostem Research Project no. 1510614, Wallonia DG06), the F.R.S.-FNRS (Epiforce Project no. T.0092.21, Cellsqueezer Project no. J.0061.23 and Optopattern Project no. U.NO26.22) and the Interreg projects ANTIRESI and MICROPLAITE, which are financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional). Y.K. and M.L. are financially supported by F.R.S.-FNRS as FRIA Grantee FNRS and Postdoctoral Fellow (Chargé de Recherches), respectively. Y.K. and S.G. acknowledge le Fonds pour la Recherche Médicale dans le Hainaut (FRMH). G.C. was supported by a grant from the Biotechnology and Biological Sciences Research Council (grant no. BB/V007483/1).","page":"1451-1461","isi":1,"article_processing_charge":"No","citation":{"mla":"Kalukula, Yohalie, et al. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” Nature Physics, vol. 21, Springer Nature, 2025, pp. 1451–61, doi:10.1038/s41567-025-02980-z.","ieee":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, and S. Gabriele, “The actin cortex acts as a mechanical memory of morphology in confined migrating cells,” Nature Physics, vol. 21. Springer Nature, pp. 1451–1461, 2025.","chicago":"Kalukula, Yohalie, Marine Luciano, Gleb Simanov, Guillaume Charras, David Brückner, and Sylvain Gabriele. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” Nature Physics. Springer Nature, 2025. https://doi.org/10.1038/s41567-025-02980-z.","ista":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. 2025. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. Nature Physics. 21, 1451–1461.","apa":"Kalukula, Y., Luciano, M., Simanov, G., Charras, G., Brückner, D., & Gabriele, S. (2025). The actin cortex acts as a mechanical memory of morphology in confined migrating cells. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-02980-z","ama":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. Nature Physics. 2025;21:1451-1461. doi:10.1038/s41567-025-02980-z","short":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele, Nature Physics 21 (2025) 1451–1461."},"author":[{"first_name":"Yohalie","last_name":"Kalukula","full_name":"Kalukula, Yohalie"},{"last_name":"Luciano","first_name":"Marine","full_name":"Luciano, Marine"},{"first_name":"Gleb","last_name":"Simanov","full_name":"Simanov, Gleb"},{"first_name":"Guillaume","last_name":"Charras","full_name":"Charras, Guillaume"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022"}],"language":[{"iso":"eng"}]}]