--- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18848' abstract: - lang: eng text: Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases. acknowledgement: We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for assistance with the figures. We thank M. Hooper for assistance developing the GFP assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory at UT Austin. This work was funded, in part, by a sponsored research agreement with Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T), and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious Diseases (NIAID 1R01AI110577 to K.A.J.). article_number: '457' article_processing_charge: Yes article_type: original author: - first_name: Rodrigo Fregoso full_name: Ocampo, Rodrigo Fregoso last_name: Ocampo - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Tyler L. full_name: Dangerfield, Tyler L. last_name: Dangerfield - first_name: Isabel full_name: Nocedal, Isabel last_name: Nocedal - first_name: Samatar A. full_name: Jirde, Samatar A. last_name: Jirde - first_name: Lisa M. full_name: Alexander, Lisa M. last_name: Alexander - first_name: Nicole C. full_name: Thomas, Nicole C. last_name: Thomas - first_name: Anjali full_name: Das, Anjali last_name: Das - first_name: Sarah full_name: Nielson, Sarah last_name: Nielson - first_name: Kenneth A. full_name: Johnson, Kenneth A. last_name: Johnson - first_name: Christopher T. full_name: Brown, Christopher T. last_name: Brown - first_name: Cristina N. full_name: Butterfield, Cristina N. last_name: Butterfield - first_name: Daniela S.A. full_name: Goltsman, Daniela S.A. last_name: Goltsman - first_name: David W. full_name: Taylor, David W. last_name: Taylor citation: ama: Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. 2025;16. doi:10.1038/s41467-024-55573-4 apa: Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S. A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55573-4 chicago: Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield, Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55573-4. ieee: R. F. Ocampo et al., “DNA targeting by compact Cas9d and its resurrected ancestor,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. 16, 457. mla: Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” Nature Communications, vol. 16, 457, Springer Nature, 2025, doi:10.1038/s41467-024-55573-4. short: R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M. Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield, D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025). date_created: 2025-01-19T23:01:50Z date_published: 2025-01-07T00:00:00Z date_updated: 2025-07-03T11:58:22Z day: '07' ddc: - '570' department: - _id: JaBr doi: 10.1038/s41467-024-55573-4 external_id: pmid: - '39774105' file: - access_level: open_access checksum: 885e96690620790d5c9f188a1587b4cd content_type: application/pdf creator: dernst date_created: 2025-01-22T14:35:22Z date_updated: 2025-01-22T14:35:22Z file_id: '18869' file_name: 2025_NatureComm_Ocampo.pdf file_size: 5450660 relation: main_file success: 1 file_date_updated: 2025-01-22T14:35:22Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: DNA targeting by compact Cas9d and its resurrected ancestor tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18849' abstract: - lang: eng text: Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks. acknowledgement: We thank Nicholas H. Barton for his comments on the manuscript, Benjamin Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many persistently inspiring conversations. This work was supported in part by the Human Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730, and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored by the Hessian Ministry for Science and Research, Arts and Culture (HMWK). article_number: e2402925121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2402925121 apa: Sokolowski, T. R., Gregor, T., Bialek, W., & Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2402925121 chicago: Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2402925121. ieee: T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” Proceedings of the National Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025. ista: Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 122(1), e2402925121. mla: Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings of the National Academy of Sciences, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:10.1073/pnas.2402925121. short: T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' date_created: 2025-01-19T23:01:50Z date_published: 2025-01-07T00:00:00Z date_updated: 2026-02-16T12:26:51Z day: '07' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.2402925121 external_id: isi: - '001392772400001' pmid: - '39752518' file: - access_level: open_access checksum: 8dbfc7d495413340225ebfae69b0cf9a content_type: application/pdf creator: dernst date_created: 2025-01-20T10:10:04Z date_updated: 2025-01-20T10:10:04Z file_id: '18862' file_name: 2025_PNAS_Sokolowski.pdf file_size: 19073585 relation: main_file success: 1 file_date_updated: 2025-01-20T10:10:04Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' name: 'Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos' - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Deriving a genetic regulatory network from an optimization principle tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2025' ... --- APC_amount: 3261,23 EUR OA_place: publisher OA_type: hybrid _id: '18850' abstract: - lang: eng text: 'Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.' acknowledgement: M.L.P. was supported by the European Molecular Biology Laboratory (EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie SkÅ‚odowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported by EMBL Core Funding and Theory@EMBL. This work is supported by European Research Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély, for helpful feedback and discussion. We also thank EMBL IT Services for the use of high performance computing resources. article_number: e2411887121 article_processing_charge: No article_type: original author: - first_name: Mindy Liu full_name: Perkins, Mindy Liu last_name: Perkins - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2411887121 apa: Perkins, M. L., Crocker, J., & Tkačik, G. (2025). Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2411887121 chicago: Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2411887121. ieee: M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” Proceedings of the National Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025. ista: Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 122(1), e2411887121. mla: Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings of the National Academy of Sciences, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025, doi:10.1073/pnas.2411887121. short: M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' date_created: 2025-01-19T23:01:51Z date_published: 2025-01-07T00:00:00Z date_updated: 2026-05-06T12:43:59Z day: '07' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.2411887121 external_id: isi: - '001392765300001' pmid: - '39793086' file: - access_level: open_access checksum: 86a8d25a6e282aeb4128f1d0b86ff911 content_type: application/pdf creator: dernst date_created: 2025-01-20T09:38:32Z date_updated: 2025-01-20T09:38:32Z file_id: '18859' file_name: 2025_PNAS_Perkins.pdf file_size: 30943709 relation: main_file success: 1 file_date_updated: 2025-01-20T09:38:32Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' name: 'Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos' publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/officerredshirt/network_crosstalk scopus_import: '1' status: public title: Chromatin enables precise and scalable gene regulation with factors of limited specificity tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18851' abstract: - lang: eng text: 'We present volume-limited samples of cataclysmic variables (CVs) and AM CVn binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray + optical color–color diagram (the "X-ray Main Sequence"). This tool identifies all CV subtypes, including magnetic and low-accretion rate systems, in contrast to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also present CV candidates out to 300 pc and 1000 pc. We discovered two previously unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030 erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7 ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the solar neighborhood. Our uniform selection method also allows us to place meaningful estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3. Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively. This work, through a novel discovery technique, shows that the observed number densities of CVs and AM CVns, as well as the fraction of period bouncers, are still in tension with population synthesis estimates.' acknowledgement: "We thank Roman Krivonos for insightful feedback, Kevin Burdge, Dovi Poznanski, and Jim Fuller for useful discussions, and Sunny Wong for providing AM CVn evolutionary models. A.C.R. acknowledges support from an NSF Graduate Fellowship.\r\n\r\nA.C.R. thanks the LSST-DA Data Science Fellowship Program, which is funded by LSST-DA, the Brinson Foundation, and the Moore Foundation; his participation in the program has benefited this work. RLO is a Research Fellow of the Brazilian institution CNPq (PQ-315632/2023-2).\r\n\r\nThis work is based on data from eROSITA, the soft X-ray instrument aboard SRG, a joint Russian-German science mission supported by the Russian Space Agency (Roskosmos), in the interests of the Russian Academy of Sciences represented by its Space Research Institute (IKI), and the Deutsches Zentrum für Luft- und Raumfahrt (DLR). The SRG spacecraft was built by Lavochkin Association (NPOL) and its subcontractors, and is operated by NPOL with support from the Max Planck Institute for Extraterrestrial Physics (MPE). The development and construction of the eROSITA X-ray instrument was led by MPE, with contributions from the Dr. Karl Remeis Observatory Bamberg & ECAP (FAU Erlangen-Nuernberg), the University of Hamburg Observatory, the Leibniz Institute for Astrophysics Potsdam (AIP), and the Institute for Astronomy and Astrophysics of the University of Tübingen, with the support of DLR and the Max Planck Society. The Argelander Institute for Astronomy of the University of Bonn and the Ludwig Maximilians Universität Munich also participated in the science preparation for eROSITA.\r\n\r\nThis work presents results from the European Space Agency (ESA) space mission Gaia. Gaia data are being processed by the Gaia Data Processing and Analysis Consortium (DPAC). Funding for the DPAC is provided by national institutions, in particular the institutions participating in the Gaia MultiLateral Agreement (MLA). The Gaia mission website is https://www.cosmos.esa.int/gaia. The Gaia archive website is https://archives.esac.esa.int/gaia.\r\n\r\nSome of the data presented herein were obtained at Keck Observatory, which is a private 501(c)3 non-profit organization operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the Native Hawaiian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We are also grateful to the staff of Palomar Observatory and that of Lick Observatory for their assistance in carrying out observations used in this work.\r\n\r\nBased on observations obtained with the Samuel Oschin Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory as part of the Zwicky Transient Facility project. ZTF is supported by the National Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration including current partners Caltech, IPAC, the Weizmann Institute of Science, the Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan, the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern University and former partners the University of Washington, Los Alamos National Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted by COO, IPAC, and UW.\r\n\r\nSoftware: used: Python and the following libraries: matplotlib (Hunter 2007), scipy (Virtanen et al. 2020), astropy (Astropy Collaboration et al. 2013), numpy (van der Walt et al. 2011). PypeIt (Prochaska et al. 2020), lpipe (Perley 2019), and Tool for OPerations on Catalogues And Tables (TOPCAT) (Taylor 2005)." article_number: '014201' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Antonio C. full_name: Rodriguez, Antonio C. last_name: Rodriguez - first_name: Kareem full_name: El-Badry, Kareem last_name: El-Badry - first_name: Valery full_name: Suleimanov, Valery last_name: Suleimanov - first_name: Anna F. full_name: Pala, Anna F. last_name: Pala - first_name: Shrinivas R. full_name: Kulkarni, Shrinivas R. last_name: Kulkarni - first_name: Boris full_name: Gaensicke, Boris last_name: Gaensicke - first_name: Kaya full_name: Mori, Kaya last_name: Mori - first_name: R. Michael full_name: Rich, R. Michael last_name: Rich - first_name: Arnab full_name: Sarkar, Arnab last_name: Sarkar - first_name: Tong full_name: Bao, Tong last_name: Bao - first_name: Raimundo Lopes full_name: De Oliveira, Raimundo Lopes last_name: De Oliveira - first_name: Gavin full_name: Ramsay, Gavin last_name: Ramsay - first_name: Paula full_name: Szkody, Paula last_name: Szkody - first_name: Matthew full_name: Graham, Matthew last_name: Graham - first_name: Thomas A. full_name: Prince, Thomas A. last_name: Prince - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Zachary P. full_name: Vanderbosch, Zachary P. last_name: Vanderbosch - first_name: Jan Van full_name: Roestel, Jan Van last_name: Roestel - first_name: Kaustav K. full_name: Das, Kaustav K. last_name: Das - first_name: Yu Jing full_name: Qin, Yu Jing last_name: Qin - first_name: Mansi M. full_name: Kasliwal, Mansi M. last_name: Kasliwal - first_name: Avery full_name: Wold, Avery last_name: Wold - first_name: Steven L. full_name: Groom, Steven L. last_name: Groom - first_name: Daniel full_name: Reiley, Daniel last_name: Reiley - first_name: Reed full_name: Riddle, Reed last_name: Riddle citation: ama: 'Rodriguez AC, El-Badry K, Suleimanov V, et al. Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities. Publications of the Astronomical Society of the Pacific. 2025;137(1). doi:10.1088/1538-3873/ada185' apa: 'Rodriguez, A. C., El-Badry, K., Suleimanov, V., Pala, A. F., Kulkarni, S. R., Gaensicke, B., … Riddle, R. (2025). Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities. Publications of the Astronomical Society of the Pacific. IOP Publishing. https://doi.org/10.1088/1538-3873/ada185' chicago: 'Rodriguez, Antonio C., Kareem El-Badry, Valery Suleimanov, Anna F. Pala, Shrinivas R. Kulkarni, Boris Gaensicke, Kaya Mori, et al. “Cataclysmic Variables and AM CVn Binaries in SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity Functions, and Space Densities.” Publications of the Astronomical Society of the Pacific. IOP Publishing, 2025. https://doi.org/10.1088/1538-3873/ada185.' ieee: 'A. C. Rodriguez et al., “Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities,” Publications of the Astronomical Society of the Pacific, vol. 137, no. 1. IOP Publishing, 2025.' ista: 'Rodriguez AC, El-Badry K, Suleimanov V, Pala AF, Kulkarni SR, Gaensicke B, Mori K, Rich RM, Sarkar A, Bao T, De Oliveira RL, Ramsay G, Szkody P, Graham M, Prince TA, Caiazzo I, Vanderbosch ZP, Roestel JV, Das KK, Qin YJ, Kasliwal MM, Wold A, Groom SL, Reiley D, Riddle R. 2025. Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities. Publications of the Astronomical Society of the Pacific. 137(1), 014201.' mla: 'Rodriguez, Antonio C., et al. “Cataclysmic Variables and AM CVn Binaries in SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity Functions, and Space Densities.” Publications of the Astronomical Society of the Pacific, vol. 137, no. 1, 014201, IOP Publishing, 2025, doi:10.1088/1538-3873/ada185.' short: A.C. Rodriguez, K. El-Badry, V. Suleimanov, A.F. Pala, S.R. Kulkarni, B. Gaensicke, K. Mori, R.M. Rich, A. Sarkar, T. Bao, R.L. De Oliveira, G. Ramsay, P. Szkody, M. Graham, T.A. Prince, I. Caiazzo, Z.P. Vanderbosch, J.V. Roestel, K.K. Das, Y.J. Qin, M.M. Kasliwal, A. Wold, S.L. Groom, D. Reiley, R. Riddle, Publications of the Astronomical Society of the Pacific 137 (2025). date_created: 2025-01-19T23:01:51Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-02-27T12:46:32Z day: '01' ddc: - '520' department: - _id: IlCa doi: 10.1088/1538-3873/ada185 external_id: arxiv: - '2408.16053' isi: - '001393204700001' file: - access_level: open_access checksum: 02a9be04a6704fc272ed5a976e5fa8c5 content_type: application/pdf creator: dernst date_created: 2025-01-20T09:52:34Z date_updated: 2025-01-20T09:52:34Z file_id: '18860' file_name: 2025_PASP_Rodriguez.pdf file_size: 5155631 relation: main_file success: 1 file_date_updated: 2025-01-20T09:52:34Z has_accepted_license: '1' intvolume: ' 137' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '01' oa: 1 oa_version: Published Version publication: Publications of the Astronomical Society of the Pacific publication_identifier: issn: - 0004-6280 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 137 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '18852' abstract: - lang: eng text: 'Recent observations have found a growing number of hypervelocity stars with speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear supernovae in white dwarf binaries. Most of the observed hypervelocity runaways in this class display a surprising inflated structure: their current radii are roughly an order of magnitude greater than they would have been as white dwarfs filling their Roche lobe. While many simulations exist studying the dynamical phase leading to supernova detonation in these systems, no detailed calculations of the long-term structure of the runaways have yet been performed. We used an existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary as a starting point for the evolution of these stars with the one-dimensional stellar evolution code MESA. We show that the supernova shock is not energetic enough to inflate the white dwarf over timescales longer than a few thousand years, significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙ away, our models do not experience significant interior heating, and all contract back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed inflated states requires either an additional source of significant heating or some other physics that is not yet accounted for in the subsequent evolution.' acknowledgement: 'This project was originally started as part of the Kavli Summer Program which took place in the Max Planck Institute for Astrophysics in Garching in July 2023, supported by the Kavli Foundation. We are grateful to Stephen Justham, Selma de Mink, and Jim Fuller for enriching discussions. We would like to thank the anonymous referee for their helpful report. A.B. was supported by the Deutsche Forschungsgemeinschaft (DFG) through grant GE2506/18-1. K.J.S. was supported by NASA through the Astrophysics Theory Program (80NSSC20K0544) and by NASA/ESA Hubble Space Telescope programs #15871 and #15918. W.E.K. was supported by NSF Grants OAC-2311323, AST-2206523, and NASA/ESA HST-AR-Theory HSTAR-16613.002-A. K.E. was supported in part by HST-GO-17441.001-A. AB and ASR would like to thank Rob Farmer for his support with PyMESA.' article_number: A114 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Aakash full_name: Bhat, Aakash last_name: Bhat - first_name: Evan B. full_name: Bauer, Evan B. last_name: Bauer - first_name: Rüdiger full_name: Pakmor, Rüdiger last_name: Pakmor - first_name: Ken J. full_name: Shen, Ken J. last_name: Shen - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Abinaya Swaruba full_name: Rajamuthukumar, Abinaya Swaruba last_name: Rajamuthukumar - first_name: Kareem full_name: El-Badry, Kareem last_name: El-Badry - first_name: Wolfgang E. full_name: Kerzendorf, Wolfgang E. last_name: Kerzendorf citation: ama: Bhat A, Bauer EB, Pakmor R, et al. Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics. 2025;693(1). doi:10.1051/0004-6361/202451371 apa: Bhat, A., Bauer, E. B., Pakmor, R., Shen, K. J., Caiazzo, I., Rajamuthukumar, A. S., … Kerzendorf, W. E. (2025). Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202451371 chicago: Bhat, Aakash, Evan B. Bauer, Rüdiger Pakmor, Ken J. Shen, Ilaria Caiazzo, Abinaya Swaruba Rajamuthukumar, Kareem El-Badry, and Wolfgang E. Kerzendorf. “Supernova Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White Dwarf Binaries.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202451371. ieee: A. Bhat et al., “Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries,” Astronomy & Astrophysics, vol. 693, no. 1. EDP Sciences, 2025. ista: Bhat A, Bauer EB, Pakmor R, Shen KJ, Caiazzo I, Rajamuthukumar AS, El-Badry K, Kerzendorf WE. 2025. Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics. 693(1), A114. mla: Bhat, Aakash, et al. “Supernova Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White Dwarf Binaries.” Astronomy & Astrophysics, vol. 693, no. 1, A114, EDP Sciences, 2025, doi:10.1051/0004-6361/202451371. short: A. Bhat, E.B. Bauer, R. Pakmor, K.J. Shen, I. Caiazzo, A.S. Rajamuthukumar, K. El-Badry, W.E. Kerzendorf, Astronomy & Astrophysics 693 (2025). date_created: 2025-01-19T23:01:51Z date_published: 2025-01-07T00:00:00Z date_updated: 2026-02-16T12:08:05Z day: '07' ddc: - '520' department: - _id: IlCa doi: 10.1051/0004-6361/202451371 external_id: arxiv: - '2407.03424' isi: - '001406577300001' file: - access_level: open_access checksum: e532b9c8123c29cfb0ee758e6d00453c content_type: application/pdf creator: dernst date_created: 2025-01-20T09:57:00Z date_updated: 2025-01-20T09:57:00Z file_id: '18861' file_name: 2025_AstronomyAstrophysics_Bhat.pdf file_size: 1692527 relation: main_file success: 1 file_date_updated: 2025-01-20T09:57:00Z has_accepted_license: '1' intvolume: ' 693' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 693 year: '2025' ... --- OA_type: closed access _id: '18853' abstract: - lang: eng text: Electrolyte additives are extensively validated effective in mitigating dendrite growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless, the mechanisms by which additives influence the formation and characteristics of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated. Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure and elucidate the mechanism by which these additives promote the dual reduction of anions. Through cryo-transmission electron microscopy analysis, we identified the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively mitigating parasitic reactions and enhancing Zn plating/stripping reversibility. Even under elevated current densities, the Zn anode exhibits ultra-stable longevity and ultra-high reversibility. This study provides a comprehensive understanding of the intrinsic mechanisms governing solvation structure modulation that lead to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing the performance and durability of AZIBs. acknowledged_ssus: - _id: EM-Fac - _id: NanoFab acknowledgement: The authors acknowledge financial support from the Joint Fund of Henan Province Science and Technology R&D Program (235200810097) and the Generalitat de Catalunya (2021SGR01581). This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by the Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NFF). G. Z. and J. L. thank the China Scholarship Council (CSC) for the scholarship support. article_processing_charge: No article_type: original author: - first_name: Guifang full_name: Zeng, Guifang last_name: Zeng - first_name: Qing full_name: Sun, Qing last_name: Sun - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Paulina R. full_name: Martínez-Alanis, Paulina R. last_name: Martínez-Alanis - first_name: Peng full_name: Wu, Peng last_name: Wu - first_name: Jing full_name: Li, Jing last_name: Li - first_name: Shang full_name: Wang, Shang last_name: Wang - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Yanhong full_name: Tian, Yanhong last_name: Tian - first_name: Lijie full_name: Ci, Lijie last_name: Ci - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Zeng G, Sun Q, Horta S, et al. Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode. Energy and Environmental Science. 2025;18(4):1683-1695. doi:10.1039/d4ee03750b apa: Zeng, G., Sun, Q., Horta, S., Martínez-Alanis, P. R., Wu, P., Li, J., … Cabot, A. (2025). Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode. Energy and Environmental Science. Royal Society of Chemistry. https://doi.org/10.1039/d4ee03750b chicago: Zeng, Guifang, Qing Sun, Sharona Horta, Paulina R. Martínez-Alanis, Peng Wu, Jing Li, Shang Wang, et al. “Modulating the Solvation Structure to Enhance Amorphous Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc Anode.” Energy and Environmental Science. Royal Society of Chemistry, 2025. https://doi.org/10.1039/d4ee03750b. ieee: G. Zeng et al., “Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode,” Energy and Environmental Science, vol. 18, no. 4. Royal Society of Chemistry, pp. 1683–1695, 2025. ista: Zeng G, Sun Q, Horta S, Martínez-Alanis PR, Wu P, Li J, Wang S, Ibáñez M, Tian Y, Ci L, Cabot A. 2025. Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode. Energy and Environmental Science. 18(4), 1683–1695. mla: Zeng, Guifang, et al. “Modulating the Solvation Structure to Enhance Amorphous Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc Anode.” Energy and Environmental Science, vol. 18, no. 4, Royal Society of Chemistry, 2025, pp. 1683–95, doi:10.1039/d4ee03750b. short: G. Zeng, Q. Sun, S. Horta, P.R. Martínez-Alanis, P. Wu, J. Li, S. Wang, M. Ibáñez, Y. Tian, L. Ci, A. Cabot, Energy and Environmental Science 18 (2025) 1683–1695. date_created: 2025-01-19T23:01:52Z date_published: 2025-02-21T00:00:00Z date_updated: 2025-07-10T11:51:27Z day: '21' department: - _id: MaIb doi: 10.1039/d4ee03750b external_id: isi: - '001389898000001' intvolume: ' 18' isi: 1 issue: '4' language: - iso: eng month: '02' oa_version: None page: 1683-1695 publication: Energy and Environmental Science publication_identifier: eissn: - 1754-5706 issn: - 1754-5692 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '18854' abstract: - lang: eng text: "Context. One of the surprising early findings with JWST has been the discovery of a strong “roll-over” or a softening of the absorption edge of Lyα in a large number of galaxies at z ≳ 6, in addition to systematic offsets from photometric redshift estimates and fundamental galaxy scaling relations. This has been interpreted as strong cumulative damped Lyα absorption (DLA) wings from high column densities of neutral atomic hydrogen (H I), signifying major gas accretion events in the formation of these galaxies.\r\nAims. To explore this new phenomenon systematically, we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and gas in and around galaxies during the reionization epoch.\r\nMethods. We characterized this benchmark sample in full and spectroscopically derived the galaxy redshifts, metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net effect of Lyα emission strength, the H I fraction in the intergalactic medium, or the local H I column density for each source. The JWST-PRIMAL survey is based on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this paper, detailing the reduction methods, the post-processing steps, and basic analysis tools. All the software, reduced spectra, and spectroscopically derived quantities and catalogs are made publicly available in dedicated repositories.\r\nResults. We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2 only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly, the prevalence and prominence of Lyα emission is found to increase with decreasing redshift, in qualitative agreement with previous observational results. Strong Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with a variety of intrinsic physical properties, but predominantly at high redshifts and low metallicities.\r\nConclusions. Our results indicate that strong DLAs likely reflect a particular early assembly phase of reionization-era galaxies, at which point they are largely dominated by pristine H I gas accretion. At z = 8 − 10, this gas gradually cools and forms into stars that ionize their local surroundings, forming large ionized bubbles and producing strong observed Lyα emission at z < 8." acknowledgement: 'We would like to thank the referee for a detailed and constructive report, greatly improving the presentation of the results in this work. We would like to thank Peter Jakobsen for his vision and heroic endeavor in optimally designing the JWST/NIRSpec instrument and some of its first on-sky observations and for enlightening discussions about the intricacies of the NIRSpec data. Further, we would like to thank John Chisholm for helpful clarifications and discussions related to the escape fraction of ionizing photons and Aayush Saxena for enlightening conversations on the escape and absorption of Lyman-α photons. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140. The data products presented herein were retrieved from the DAWN JWST Archive (DJA). DJA is an initiative of the Cosmic Dawn Center, which is funded by the Danish National Research Foundation under grant DNRF140. P.D. acknowledge support from the NWO grant 016.VIDI.189.162 (“ODIN") and warmly thanks the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. Support from the ERC Advanced Grant INTERSTELLAR H2020/740120 is kindly acknowledged (A.F.). S.G. acknowledges financial support from the Villum Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. M.K. was supported by the ANID BASAL project FB210003. G.E.M. acknowledges financial support from the Villum Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. J.W. acknowledges support from the Science and Technology Facilities Council (STFC), by the ERC through Advanced Grant 695671 “QUENCH”, by the UKRI Frontier Research grant RISEandFALL. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. F.C. acknowledges support from a UKRI Frontier Research Guarantee Grant (PI Cullen; grant reference EP/X021025/1). J.H.W. acknowledges support by NSF grant AST-2108020 and NASA grants 80NSSC20K0520 and 80NSSC21K1053. NRT acknowledges support through STFC consolidated grant ST/W000857/1. M.J.H. is supported by the Swedish Research Council, VetenskapsrÅdet, and is fellow of the Knut & Alice Wallenberg foundation. This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes (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. Software: This work made use of and acknowledge the following software: NumPy (Harris et al. 2020), Matplotlib (Hunter 2007), LMfit (Newville et al. 2014), SciPy (Virtanen et al. 2020), grizli (Brammer 2023a), Astrodrizzle (Gonzaga et al. 2012), and MsaExp (v0.3; Brammer 2023b).' article_number: A60 article_processing_charge: No article_type: original author: - first_name: K. E. full_name: Heintz, K. E. last_name: Heintz - first_name: G. B. full_name: Brammer, G. B. last_name: Brammer - first_name: D. full_name: Watson, D. last_name: Watson - first_name: P. A. full_name: Oesch, P. A. last_name: Oesch - first_name: L. C. full_name: Keating, L. C. last_name: Keating - first_name: M. J. full_name: Hayes, M. J. last_name: Hayes - first_name: Unknown full_name: Abdurro'Uf, Unknown last_name: Abdurro'Uf - first_name: K. Z. full_name: Arellano-Córdova, K. Z. last_name: Arellano-Córdova - first_name: A. C. full_name: Carnall, A. C. last_name: Carnall - first_name: C. R. full_name: Christiansen, C. R. last_name: Christiansen - first_name: F. full_name: Cullen, F. last_name: Cullen - first_name: R. full_name: Davé, R. last_name: Davé - first_name: P. full_name: Dayal, P. last_name: Dayal - first_name: A. full_name: Ferrara, A. last_name: Ferrara - first_name: K. full_name: Finlator, K. last_name: Finlator - first_name: J. P.U. full_name: Fynbo, J. P.U. last_name: Fynbo - first_name: S. R. full_name: Flury, S. R. last_name: Flury - first_name: V. full_name: Gelli, V. last_name: Gelli - first_name: S. full_name: Gillman, S. last_name: Gillman - first_name: R. full_name: Gottumukkala, R. last_name: Gottumukkala - first_name: K. full_name: Gould, K. last_name: Gould - first_name: T. R. full_name: Greve, T. R. last_name: Greve - first_name: S. E. full_name: Hardin, S. E. last_name: Hardin - first_name: T. Y.Y. full_name: Hsiao, T. Y.Y. last_name: Hsiao - first_name: A. full_name: Hutter, A. last_name: Hutter - first_name: P. full_name: Jakobsson, P. last_name: Jakobsson - first_name: M. full_name: Killi, M. last_name: Killi - first_name: N. full_name: Khosravaninezhad, N. last_name: Khosravaninezhad - first_name: P. full_name: Laursen, P. last_name: Laursen - first_name: M. M. full_name: Lee, M. M. last_name: Lee - first_name: G. E. full_name: Magdis, G. E. last_name: Magdis - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: R. P. full_name: Naidu, R. P. last_name: Naidu - first_name: D. full_name: Narayanan, D. last_name: Narayanan - first_name: C. full_name: Pollock, C. last_name: Pollock - first_name: M. K.M. full_name: Prescott, M. K.M. last_name: Prescott - first_name: V. full_name: Rusakov, V. last_name: Rusakov - first_name: M. full_name: Shuntov, M. last_name: Shuntov - first_name: A. full_name: Sneppen, A. last_name: Sneppen - first_name: R. full_name: Smit, R. last_name: Smit - first_name: N. R. full_name: Tanvir, N. R. last_name: Tanvir - first_name: C. full_name: Terp, C. last_name: Terp - first_name: S. full_name: Toft, S. last_name: Toft - first_name: F. full_name: Valentino, F. last_name: Valentino - first_name: A. P. full_name: Vijayan, A. P. last_name: Vijayan - first_name: J. R. full_name: Weaver, J. R. last_name: Weaver - first_name: J. H. full_name: Wise, J. H. last_name: Wise - first_name: J. full_name: Witstok, J. last_name: Witstok citation: ama: 'Heintz KE, Brammer GB, Watson D, et al. The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy & Astrophysics. 2025;693. doi:10.1051/0004-6361/202450243' apa: 'Heintz, K. E., Brammer, G. B., Watson, D., Oesch, P. A., Keating, L. C., Hayes, M. J., … Witstok, J. (2025). The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202450243' chicago: 'Heintz, K. E., G. B. Brammer, D. Watson, P. A. Oesch, L. C. Keating, M. J. Hayes, Unknown Abdurro’Uf, et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec Reference Sample for the Physical Properties and Lyman-α Absorption and Emission of ∼600 Galaxies at z = 5.0-13.4.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202450243.' ieee: 'K. E. Heintz et al., “The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4,” Astronomy & Astrophysics, vol. 693. EDP Sciences, 2025.' ista: 'Heintz KE, Brammer GB, Watson D, Oesch PA, Keating LC, Hayes MJ, Abdurro’Uf U, Arellano-Córdova KZ, Carnall AC, Christiansen CR, Cullen F, Davé R, Dayal P, Ferrara A, Finlator K, Fynbo JPU, Flury SR, Gelli V, Gillman S, Gottumukkala R, Gould K, Greve TR, Hardin SE, Hsiao TYY, Hutter A, Jakobsson P, Killi M, Khosravaninezhad N, Laursen P, Lee MM, Magdis GE, Matthee JJ, Naidu RP, Narayanan D, Pollock C, Prescott MKM, Rusakov V, Shuntov M, Sneppen A, Smit R, Tanvir NR, Terp C, Toft S, Valentino F, Vijayan AP, Weaver JR, Wise JH, Witstok J. 2025. The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy & Astrophysics. 693, A60.' mla: 'Heintz, K. E., et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec Reference Sample for the Physical Properties and Lyman-α Absorption and Emission of ∼600 Galaxies at z = 5.0-13.4.” Astronomy & Astrophysics, vol. 693, A60, EDP Sciences, 2025, doi:10.1051/0004-6361/202450243.' short: K.E. Heintz, G.B. Brammer, D. Watson, P.A. Oesch, L.C. Keating, M.J. Hayes, U. Abdurro’Uf, K.Z. Arellano-Córdova, A.C. Carnall, C.R. Christiansen, F. Cullen, R. Davé, P. Dayal, A. Ferrara, K. Finlator, J.P.U. Fynbo, S.R. Flury, V. Gelli, S. Gillman, R. Gottumukkala, K. Gould, T.R. Greve, S.E. Hardin, T.Y.Y. Hsiao, A. Hutter, P. Jakobsson, M. Killi, N. Khosravaninezhad, P. Laursen, M.M. Lee, G.E. Magdis, J.J. Matthee, R.P. Naidu, D. Narayanan, C. Pollock, M.K.M. Prescott, V. Rusakov, M. Shuntov, A. Sneppen, R. Smit, N.R. Tanvir, C. Terp, S. Toft, F. Valentino, A.P. Vijayan, J.R. Weaver, J.H. Wise, J. Witstok, Astronomy & Astrophysics 693 (2025). date_created: 2025-01-19T23:01:52Z date_published: 2025-01-06T00:00:00Z date_updated: 2026-02-16T12:07:37Z day: '06' ddc: - '520' department: - _id: JoMa doi: 10.1051/0004-6361/202450243 external_id: isi: - '001390856800001' file: - access_level: open_access checksum: 67a791080ade9bfb449d249de2af7456 content_type: application/pdf creator: dernst date_created: 2025-01-20T09:17:33Z date_updated: 2025-01-20T09:17:33Z file_id: '18858' file_name: 2025_AstronomyAstrophysics_Heintz.pdf file_size: 4513466 relation: main_file success: 1 file_date_updated: 2025-01-20T09:17:33Z has_accepted_license: '1' intvolume: ' 693' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4' tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 693 year: '2025' ... --- OA_place: repository OA_type: green _id: '18855' abstract: - lang: eng text: "A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function, which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector of pre-image counts c_x=|H^-1(x)|.\r\nWe develop black-box sampling algorithms to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min) \ (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max) and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of n and q up to logarithmic terms." acknowledgement: "We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, and Maksym Serbyn for bringing to our attention the WL algorithm and its use in physics.\r\nThis is an extended version, which includes work under the same name from ICALP 2023, as well as the earlier work [22] appearing in COLT 2018.\r\nV. Kolmogorov was supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160" article_number: '3' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: David G. full_name: Harris, David G. last_name: Harris - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. ACM Transactions on Algorithms. 2025;21(1). doi:10.1145/3685676 apa: Harris, D. G., & Kolmogorov, V. (2025). Parameter estimation for Gibbs distributions. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3685676 chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” ACM Transactions on Algorithms. Association for Computing Machinery, 2025. https://doi.org/10.1145/3685676. ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” ACM Transactions on Algorithms, vol. 21, no. 1. Association for Computing Machinery, 2025. ista: Harris DG, Kolmogorov V. 2025. Parameter estimation for Gibbs distributions. ACM Transactions on Algorithms. 21(1), 3. mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” ACM Transactions on Algorithms, vol. 21, no. 1, 3, Association for Computing Machinery, 2025, doi:10.1145/3685676. short: D.G. Harris, V. Kolmogorov, ACM Transactions on Algorithms 21 (2025). corr_author: '1' date_created: 2025-01-19T23:01:52Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-07-10T11:50:44Z day: '01' department: - _id: VlKo doi: 10.1145/3685676 ec_funded: 1 external_id: arxiv: - '2007.10824' isi: - '001399998600008' intvolume: ' 21' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2007.10824 month: '01' oa: 1 oa_version: Preprint project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: ACM Transactions on Algorithms publication_identifier: eissn: - 1549-6333 issn: - 1549-6325 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '14084' relation: earlier_version status: public scopus_import: '1' status: public title: Parameter estimation for Gibbs distributions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '18866' abstract: - lang: eng text: Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ, (or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion membership down to F322W2 ∼ 27. We identified an intriguing feature at the very low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24 and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent discontinuity in the slope of the main sequence. A similar discontinuity is seen in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset of absorption. We therefore hypothesize that the cluster hosts disproportionately more oxygen-poor stars near the bottom of the main sequence compared to the upper main sequence and the red giant branch. Our results show no strong or conclusive evidence of a rise in the brown dwarf luminosity function at faint magnitudes, in contrast to previous findings likely affected by faint red background galaxies. In our analysis, we accounted for this contamination by using proper motion membership. acknowledgement: We dedicate this paper to the memory of our colleague Prof. Harvey Richer (⋆ April 1944 —† 13 November 2023), a highly accomplished astronomer and expert in stellar populations and in particular within globular clusters, who passed away during this project. Harvey grew up in Montreal and was at least the second star man to graduate from his high school, having been preceded by William Shatner by more than a decade. He worked at the University of British Columbia for most of his career, and his focus was the late stages of stellar evolution, in particular carbon stars and white dwarfs. We thank the referee for his valuable suggestions and comments, which helped improve the paper, as well as for his prompt revision. article_number: A68 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: M. full_name: Scalco, M. last_name: Scalco - first_name: R. full_name: Gerasimov, R. last_name: Gerasimov - first_name: L. R. full_name: Bedin, L. R. last_name: Bedin - first_name: E. full_name: Vesperini, E. last_name: Vesperini - first_name: M. full_name: Correnti, M. last_name: Correnti - first_name: D. full_name: Nardiello, D. last_name: Nardiello - first_name: A. full_name: Burgasser, A. last_name: Burgasser - first_name: H. full_name: Richer, H. last_name: Richer - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: J. full_name: Heyl, J. last_name: Heyl - first_name: M. full_name: Libralato, M. last_name: Libralato - first_name: J. full_name: Anderson, J. last_name: Anderson - first_name: M. full_name: Griggio, M. last_name: Griggio citation: ama: Scalco M, Gerasimov R, Bedin LR, et al. JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition. Astronomy & Astrophysics. 2025;694. doi:10.1051/0004-6361/202452907 apa: Scalco, M., Gerasimov, R., Bedin, L. R., Vesperini, E., Correnti, M., Nardiello, D., … Griggio, M. (2025). JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202452907 chicago: Scalco, M., R. Gerasimov, L. R. Bedin, E. Vesperini, M. Correnti, D. Nardiello, A. Burgasser, et al. “JWST Photometry and Astrometry of 47 Tucanae. Discontinuity in the Stellar Sequence at the Star--Brown Dwarf Transition.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202452907. ieee: M. Scalco et al., “JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition,” Astronomy & Astrophysics, vol. 694. EDP Sciences, 2025. ista: Scalco M, Gerasimov R, Bedin LR, Vesperini E, Correnti M, Nardiello D, Burgasser A, Richer H, Caiazzo I, Heyl J, Libralato M, Anderson J, Griggio M. 2025. JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition. Astronomy & Astrophysics. 694, A68. mla: Scalco, M., et al. “JWST Photometry and Astrometry of 47 Tucanae. Discontinuity in the Stellar Sequence at the Star--Brown Dwarf Transition.” Astronomy & Astrophysics, vol. 694, A68, EDP Sciences, 2025, doi:10.1051/0004-6361/202452907. short: M. Scalco, R. Gerasimov, L.R. Bedin, E. Vesperini, M. Correnti, D. Nardiello, A. Burgasser, H. Richer, I. Caiazzo, J. Heyl, M. Libralato, J. Anderson, M. Griggio, Astronomy & Astrophysics 694 (2025). date_created: 2025-01-21T15:29:36Z date_published: 2025-02-04T00:00:00Z date_updated: 2025-07-10T11:51:28Z day: '04' ddc: - '520' department: - _id: IlCa doi: 10.1051/0004-6361/202452907 external_id: arxiv: - '2501.04446' isi: - '001414753300007' file: - access_level: open_access checksum: db765ce222df60a1e7c19da1968906a8 content_type: application/pdf creator: dernst date_created: 2025-04-16T07:13:31Z date_updated: 2025-04-16T07:13:31Z file_id: '19569' file_name: 2025_AstronomyAstrophysics_Scalco.pdf file_size: 18080704 relation: main_file success: 1 file_date_updated: 2025-04-16T07:13:31Z has_accepted_license: '1' intvolume: ' 694' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 694 year: '2025' ... --- OA_type: closed access _id: '18878' abstract: - lang: eng text: Thermoelectric (TE) materials, with the ability to convert heat into electrical energy, can generate micro-electrical fields at electronic interfaces with biological systems, making them applicable in electric-catalyzing as nanozymes, and modulate the infected microenvironment of skin wounds. Thereby, by harnessing temperature differences in vitro or in vivo, TE nanomaterials can provide antimicrobial reactive oxygen species (ROS) by catalyzing redox reactions, thereby accelerating wound healing by suppressing infection. However, despite their promising potential, there is still a lack of comprehensive understanding of the antimicrobial mechanisms, biocompatibility, and practical applications of TE nanomaterials in wound healing, as this is a newly-emerged sub-area of energy-related biomedical applications. This review aims to address this gap by highlighting the emerging progress of TE materials in wound healing, clarifying their mechanism and advances, emphasizing their potential challenges for commercialization and clinical use, and proposing novel design strategies of TE nanomaterials for effective antibacterial performance. acknowledgement: This work was financially supported by the Sichuan Science and Technology Program (Nos. 2023ZYD0064 and 2023YFG0220), the Fundamental Research Funds for the Central Universities (No. YJ202242), and the Research Funding from West China School/Hospital of Stomatology, Sichuan University (No. QDJF2022–2). article_processing_charge: No article_type: review author: - first_name: Shiyu full_name: Jia, Shiyu last_name: Jia - first_name: Cai full_name: Qi, Cai last_name: Qi - first_name: Shengduo full_name: Xu, Shengduo id: 12ab8624-4c8a-11ec-9e11-e1ac2438f22f last_name: Xu - first_name: Lei full_name: Yang, Lei last_name: Yang - first_name: Qiang full_name: Sun, Qiang last_name: Sun citation: ama: Jia S, Qi C, Xu S, Yang L, Sun Q. Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal of Materials Science and Technology. 2025;225(08):212-226. doi:10.1016/j.jmst.2024.11.039 apa: Jia, S., Qi, C., Xu, S., Yang, L., & Sun, Q. (2025). Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal of Materials Science and Technology. Elsevier. https://doi.org/10.1016/j.jmst.2024.11.039 chicago: Jia, Shiyu, Cai Qi, Shengduo Xu, Lei Yang, and Qiang Sun. “Advancements of Thermoelectric Nanomaterials in ROS-Mediated Broad-Spectrum Antibacterial Therapies for Wound Healing.” Journal of Materials Science and Technology. Elsevier, 2025. https://doi.org/10.1016/j.jmst.2024.11.039. ieee: S. Jia, C. Qi, S. Xu, L. Yang, and Q. Sun, “Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing,” Journal of Materials Science and Technology, vol. 225, no. 08. Elsevier, pp. 212–226, 2025. ista: Jia S, Qi C, Xu S, Yang L, Sun Q. 2025. Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal of Materials Science and Technology. 225(08), 212–226. mla: Jia, Shiyu, et al. “Advancements of Thermoelectric Nanomaterials in ROS-Mediated Broad-Spectrum Antibacterial Therapies for Wound Healing.” Journal of Materials Science and Technology, vol. 225, no. 08, Elsevier, 2025, pp. 212–26, doi:10.1016/j.jmst.2024.11.039. short: S. Jia, C. Qi, S. Xu, L. Yang, Q. Sun, Journal of Materials Science and Technology 225 (2025) 212–226. date_created: 2025-01-26T23:01:49Z date_published: 2025-08-01T00:00:00Z date_updated: 2025-12-30T07:19:04Z day: '01' department: - _id: MaIb doi: 10.1016/j.jmst.2024.11.039 external_id: isi: - '001407204300001' intvolume: ' 225' isi: 1 issue: '08' language: - iso: eng month: '08' oa_version: None page: 212-226 publication: Journal of Materials Science and Technology publication_identifier: issn: - 1005-0302 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 225 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18879' abstract: - lang: eng text: 'Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. ' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: ScienComp acknowledgement: We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop, and Scientific Computing. We are particularly grateful to the patient donors for their support of this project and also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha Feucht, and Ekaterina Pataraia for their clinical care of the patients included in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample donors for their support of this research. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship (to A.N.-O.). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Victor M full_name: Vargas Barroso, Victor M id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87 last_name: Vargas Barroso - first_name: Rebecca full_name: Morse, Rebecca id: ceb89ae7-dc8d-11ea-abe3-da3301d0eab4 last_name: Morse - first_name: Andrea C full_name: Navas Olivé, Andrea C id: 739d26c9-52e8-11ee-8d72-f14d3893b4ce last_name: Navas Olivé orcid: 0000-0002-9280-8597 - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Matthias full_name: Tomschik, Matthias last_name: Tomschik - first_name: Karl full_name: Rössler, Karl last_name: Rössler - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 2025;188(2):501-514.e18. doi:10.1016/j.cell.2024.11.022 apa: Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. Elsevier. https://doi.org/10.1016/j.cell.2024.11.022 chicago: Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” Cell. Elsevier, 2025. https://doi.org/10.1016/j.cell.2024.11.022. ieee: J. Watson et al., “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” Cell, vol. 188, no. 2. Elsevier, p. 501–514.e18, 2025. ista: Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18. mla: Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” Cell, vol. 188, no. 2, Elsevier, 2025, p. 501–514.e18, doi:10.1016/j.cell.2024.11.022. short: J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18. corr_author: '1' date_created: 2025-01-26T23:01:49Z date_published: 2025-01-23T00:00:00Z date_updated: 2026-04-14T08:34:32Z day: '23' ddc: - '570' department: - _id: JoDa - _id: PeJo - _id: GradSch doi: 10.1016/j.cell.2024.11.022 ec_funded: 1 external_id: isi: - '001408395600001' pmid: - '39667938' file: - access_level: open_access checksum: d5a818edc32d249cdf75e1bb5b70a4b7 content_type: application/pdf creator: dernst date_created: 2025-01-27T08:46:33Z date_updated: 2025-01-27T08:46:33Z file_id: '18884' file_name: 2025_Cell_Watson.pdf file_size: 14082343 relation: main_file success: 1 file_date_updated: 2025-01-27T08:46:33Z has_accepted_license: '1' intvolume: ' 188' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 501-514.e18 pmid: 1 project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: 8d9195e9-16d5-11f0-9cad-d075be887a1e grant_number: PAT 4178023 name: Synaptic networks of human brain - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '18688' relation: earlier_version status: public scopus_import: '1' status: public title: Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 188 year: '2025' ... --- OA_place: repository OA_type: green _id: '18880' abstract: - lang: eng text: In this paper, we provide a rate of convergence for a version of the Carathéodory convergence for the multiple SLE model with a Dyson Brownian motion driver towards its hydrodynamic limit, for β=1 and β=2. The results are obtained by combining techniques from the field of Schramm–Loewner Evolutions with modern techniques from random matrices. Our approach shows how one can apply modern tools used in the proof of universality in random matrix theory to the field of Schramm–Loewner Evolutions. article_number: '2450028' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Andrew J full_name: Campbell, Andrew J id: 582b06a9-1f1c-11ee-b076-82ffce00dde4 last_name: Campbell - first_name: Kyle full_name: Luh, Kyle last_name: Luh - first_name: Vlad full_name: Margarint, Vlad last_name: Margarint citation: ama: 'Campbell AJ, Luh K, Margarint V. Rate of convergence in multiple SLE using random matrix theory. Random Matrices: Theory and Application. 2025;14(1). doi:10.1142/S201032632450028X' apa: 'Campbell, A. J., Luh, K., & Margarint, V. (2025). Rate of convergence in multiple SLE using random matrix theory. Random Matrices: Theory and Application. World Scientific Publishing. https://doi.org/10.1142/S201032632450028X' chicago: 'Campbell, Andrew J, Kyle Luh, and Vlad Margarint. “Rate of Convergence in Multiple SLE Using Random Matrix Theory.” Random Matrices: Theory and Application. World Scientific Publishing, 2025. https://doi.org/10.1142/S201032632450028X.' ieee: 'A. J. Campbell, K. Luh, and V. Margarint, “Rate of convergence in multiple SLE using random matrix theory,” Random Matrices: Theory and Application, vol. 14, no. 1. World Scientific Publishing, 2025.' ista: 'Campbell AJ, Luh K, Margarint V. 2025. Rate of convergence in multiple SLE using random matrix theory. Random Matrices: Theory and Application. 14(1), 2450028.' mla: 'Campbell, Andrew J., et al. “Rate of Convergence in Multiple SLE Using Random Matrix Theory.” Random Matrices: Theory and Application, vol. 14, no. 1, 2450028, World Scientific Publishing, 2025, doi:10.1142/S201032632450028X.' short: 'A.J. Campbell, K. Luh, V. Margarint, Random Matrices: Theory and Application 14 (2025).' date_created: 2025-01-26T23:01:49Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-07-10T11:51:29Z day: '01' department: - _id: LaEr doi: 10.1142/S201032632450028X external_id: arxiv: - '2301.04722' isi: - '001397136000001' intvolume: ' 14' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2301.04722 month: '01' oa: 1 oa_version: Preprint publication: 'Random Matrices: Theory and Application' publication_identifier: eissn: - 2010-3271 issn: - 2010-3263 publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: Rate of convergence in multiple SLE using random matrix theory type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18881' abstract: - lang: eng text: The determination of the intrinsic properties of solid active material candidates is essential for their performance optimization. However, macroscopic electrodes and related analytical techniques show challenges concerning the number of additional influencing parameters. We explore recessed microelectrodes (rME) as a platform that allows for a binder-free investigation of Prussian Blue analogues (PBA), a family of promising battery materials. The enhanced diffusion using microelectrochemical tools is indispensable to assess the intrinsic material performance, overcoming the limitation of cation diffusion from the electrolyte to the solid interface during (dis)charging cycles and allowing the investigation of limiting steps in the coupled ion-electron transfer process. The intrinsic electrochemical performance of PBAs was studied in a three-electrode configuration by means of cyclic voltammetry and galvanostatic (dis)charging in aqueous Na+-containing electrolyte. We extended the evaluation to the role of the electrolyte on the performance of cathodic and anodic processes of a Mn-based PBA. Ex-situ and operando chemical characterization were coupled to support the microelectrochemical results. acknowledgement: The authors acknowledge funding from the European Union's Horizon Europe research and innovation programme – European Innovation Council (EIC) under the grant agreement 101046742 (MeBattery), the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (CasCat [833408]), and the Spanish Government (Ministerio de Ciencia e Innovación, Grants PID2021-124974OB-C22). The authors thank Martin Trautmann (RUB) and Prof. Dr. Daniel Grasseschi (Federal University of Rio de Janeiro – UFRJ) for support concerning ICP-MS and Raman measurements, respectively. Open Access funding enabled and organized by Projekt DEAL. article_number: e202400743 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nomnotho full_name: Jiyane, Nomnotho last_name: Jiyane - first_name: Carla full_name: Santana Santos, Carla last_name: Santana Santos - first_name: Igor full_name: Echevarria Poza, Igor id: fbae1d3b-8142-11ed-8927-a8cf34feb495 last_name: Echevarria Poza - first_name: Mario full_name: Palacios Corella, Mario id: 452e82c6-803f-11ed-ab7e-ca0439e73a5d last_name: Palacios Corella - first_name: Muhammad Adib full_name: Abdillah Mahbub, Muhammad Adib last_name: Abdillah Mahbub - first_name: Gimena full_name: Marin-Tajadura, Gimena last_name: Marin-Tajadura - first_name: Thomas full_name: Quast, Thomas last_name: Quast - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Edgar full_name: Ventosa, Edgar last_name: Ventosa - first_name: Wolfgang full_name: Schuhmann, Wolfgang last_name: Schuhmann citation: ama: Jiyane N, Santana Santos C, Echevarria Poza I, et al. Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application. Batteries & Supercaps. 2025;8(3). doi:10.1002/batt.202400743 apa: Jiyane, N., Santana Santos, C., Echevarria Poza, I., Palacios Corella, M., Abdillah Mahbub, M. A., Marin-Tajadura, G., … Schuhmann, W. (2025). Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application. Batteries & Supercaps. Wiley. https://doi.org/10.1002/batt.202400743 chicago: Jiyane, Nomnotho, Carla Santana Santos, Igor Echevarria Poza, Mario Palacios Corella, Muhammad Adib Abdillah Mahbub, Gimena Marin-Tajadura, Thomas Quast, Maria Ibáñez, Edgar Ventosa, and Wolfgang Schuhmann. “Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application.” Batteries & Supercaps. Wiley, 2025. https://doi.org/10.1002/batt.202400743. ieee: N. Jiyane et al., “Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application,” Batteries & Supercaps, vol. 8, no. 3. Wiley, 2025. ista: Jiyane N, Santana Santos C, Echevarria Poza I, Palacios Corella M, Abdillah Mahbub MA, Marin-Tajadura G, Quast T, Ibáñez M, Ventosa E, Schuhmann W. 2025. Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application. Batteries & Supercaps. 8(3), e202400743. mla: Jiyane, Nomnotho, et al. “Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application.” Batteries & Supercaps, vol. 8, no. 3, e202400743, Wiley, 2025, doi:10.1002/batt.202400743. short: N. Jiyane, C. Santana Santos, I. Echevarria Poza, M. Palacios Corella, M.A. Abdillah Mahbub, G. Marin-Tajadura, T. Quast, M. Ibáñez, E. Ventosa, W. Schuhmann, Batteries & Supercaps 8 (2025). date_created: 2025-01-26T23:01:50Z date_published: 2025-03-01T00:00:00Z date_updated: 2026-02-16T12:15:59Z day: '01' ddc: - '540' department: - _id: MaIb doi: 10.1002/batt.202400743 external_id: isi: - '001402369200001' file: - access_level: open_access checksum: a9ebdb25c43dc2823cc8a1ba9154d914 content_type: application/pdf creator: dernst date_created: 2025-04-16T06:47:09Z date_updated: 2025-04-16T06:47:09Z file_id: '19568' file_name: 2025_Batteries_Jiyane.pdf file_size: 1251786 relation: main_file success: 1 file_date_updated: 2025-04-16T06:47:09Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '03' oa: 1 oa_version: Published Version publication: Batteries & Supercaps publication_identifier: eissn: - 2566-6223 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2025' ... --- OA_type: closed access _id: '18882' abstract: - lang: eng text: Ternary liquid-like thermoelectric materials have garnered significant attention due to their ultra-low lattice thermal conductivity. Among these, Ag8SnSe6 stands out for its exceptionally low sound velocity and thermal conductivity. However, the inherent poor electrical conductivity and suboptimal thermoelectric properties of Ag8SnSe6 necessitate further improvement. Here, a novel approach is initiated to enhance the thermoelectric properties of Ag8SnSe6 by combining low-dimensionalization with intrinsic doping. For the first time, this work successfully synthesizes single-phase Ag8SnSe6 nanocrystals, ≈10 nm in size, with the correct phase and composition using a robust and reliable colloidal method. This approach represents a significant improvement over previous reports on this material. Reducing the crystal domains of Ag8SnSe6 to the nanoscale induces quantum confinement effects, increasing the density of states near the Fermi surface. It also introduces additional grain boundaries, which lower the lattice thermal conductivity and simplify structural design. Moreover, incorporating small amounts of Sn nanopowder into the Ag8SnSe6 nanocrystals before consolidation further enhances the thermoelectric performance. Sn acts as a donor dopant, increasing the electronic concentration while at the same time improving their mobility by reducing interface barriers, thus significantly improving the material transport properties. Additionally, the presence of Sn leads to the formation of point defects, dislocations, and secondary phases, which increase phonon scattering and further reduce the thermal conductivity. Through this synergistic optimization, the figure of merit shows a significant increase across a wide temperature range. Overall, a strategy is presented for the controlled preparation of Ag8SnSe6 nanocrystals, the decoupling of their electrical and thermal transport, and the practical application of this material to thermoelectric single-leg modules. acknowledgement: X.Z. and M.L. contributed equally to this work. This work was supported by the National Key R&D Program of China (No. 2024YFE0105200). Also supported by the China Postdoctoral Science Foundation under Grant Number 2023M743151. M.J. acknowledges funding from the China Postdoctoral Science Foundation (No. 2023M743221). A.C. thanks the support from the projects ENE2016-77798-C4-3-R and NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. article_number: '2421449' article_processing_charge: No article_type: original author: - first_name: Xueke full_name: Zhao, Xueke last_name: Zhao - first_name: Mengyao full_name: Li, Mengyao last_name: Li - first_name: Mochen full_name: Jia, Mochen last_name: Jia - first_name: Christine full_name: Fiedler, Christine id: bd3fceba-dc74-11ea-a0a7-c17f71817366 last_name: Fiedler - first_name: Bingfei full_name: Nan, Bingfei last_name: 'Nan' - first_name: Dongwen full_name: Yang, Dongwen last_name: Yang - first_name: Lei full_name: Li, Lei last_name: Li - first_name: Zicheng full_name: Yuan, Zicheng last_name: Yuan - first_name: Hongzhang full_name: Song, Hongzhang last_name: Song - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Ziyu full_name: Wang, Ziyu last_name: Wang - first_name: Chongxin full_name: Shan, Chongxin last_name: Shan - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: Zhao X, Li M, Jia M, et al. Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance. Advanced Functional Materials. 2025;35(24). doi:10.1002/adfm.202421449 apa: Zhao, X., Li, M., Jia, M., Fiedler, C., Nan, B., Yang, D., … Cabot, A. (2025). Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance. Advanced Functional Materials. Wiley. https://doi.org/10.1002/adfm.202421449 chicago: Zhao, Xueke, Mengyao Li, Mochen Jia, Christine Fiedler, Bingfei Nan, Dongwen Yang, Lei Li, et al. “Low-Dimensional Structure Modulation in Ag8SnSe6 for Enhanced Thermoelectric Performance.” Advanced Functional Materials. Wiley, 2025. https://doi.org/10.1002/adfm.202421449. ieee: X. Zhao et al., “Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance,” Advanced Functional Materials, vol. 35, no. 24. Wiley, 2025. ista: Zhao X, Li M, Jia M, Fiedler C, Nan B, Yang D, Li L, Yuan Z, Song H, Liu Y, Ibáñez M, Wang Z, Shan C, Cabot A. 2025. Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance. Advanced Functional Materials. 35(24), 2421449. mla: Zhao, Xueke, et al. “Low-Dimensional Structure Modulation in Ag8SnSe6 for Enhanced Thermoelectric Performance.” Advanced Functional Materials, vol. 35, no. 24, 2421449, Wiley, 2025, doi:10.1002/adfm.202421449. short: X. Zhao, M. Li, M. Jia, C. Fiedler, B. Nan, D. Yang, L. Li, Z. Yuan, H. Song, Y. Liu, M. Ibáñez, Z. Wang, C. Shan, A. Cabot, Advanced Functional Materials 35 (2025). date_created: 2025-01-26T23:01:50Z date_published: 2025-06-19T00:00:00Z date_updated: 2025-12-30T07:17:39Z day: '19' department: - _id: MaIb - _id: GradSch doi: 10.1002/adfm.202421449 external_id: isi: - '001398067000001' intvolume: ' 35' isi: 1 issue: '24' language: - iso: eng month: '06' oa_version: None publication: Advanced Functional Materials publication_identifier: eissn: - 1616-3028 issn: - 1616-301X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2025' ... --- OA_place: repository OA_type: gold _id: '18886' abstract: - lang: eng text: Research Data for publication 'Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors' acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: 'We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. We thank Simon Robson for proofreading the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the HORIZON-RIA 101069515 project. This research was funded in whole or in part by the Austrian Science Fund (FWF) DOI:10.55776/P32235, DOI:10.55776/I5060 and DOI:10.55776/P36507. For Open Access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. M.J. acknowledges funding from FellowQUTE 2024-01. I.M.P. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG – German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC''s Quantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors acknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development Fund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM.' article_processing_charge: No author: - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 citation: ama: Janik M. Research data for publication “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors.” 2025. doi:10.15479/AT:ISTA:18886 apa: Janik, M. (2025). Research data for publication “Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18886 chicago: Janik, Marian. “Research Data for Publication ‘Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18886. ieee: M. Janik, “Research data for publication ‘Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors.’” Institute of Science and Technology Austria, 2025. ista: Janik M. 2025. Research data for publication ‘Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18886. mla: Janik, Marian. Research Data for Publication “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:18886. short: M. Janik, (2025). contributor: - contributor_type: researcher first_name: Kevin Etienne Robert id: 53f93ea2-803f-11ed-ab7e-b283135794ef last_name: Roux - contributor_type: researcher first_name: Carla N id: 18777c01-896a-11ed-bdf8-e4851dc07d16 last_name: Borja Espinosa - contributor_type: researcher first_name: Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - contributor_type: researcher first_name: Abdulhamid id: 160D87FA-96B5-11E9-BF77-7626E6697425 last_name: Baghdadi - contributor_type: researcher first_name: Thomas id: 38756BB2-F248-11E8-B48F-1D18A9856A87 last_name: Adletzberger - contributor_type: researcher first_name: Stefano last_name: Calcaterra - contributor_type: researcher first_name: Marc last_name: Botifoll - contributor_type: researcher first_name: Alba Garzón last_name: Manjón - contributor_type: researcher first_name: Jordi last_name: Arbiol - contributor_type: researcher first_name: Daniel last_name: Chrastina - contributor_type: researcher first_name: Giovanni last_name: Isella - contributor_type: researcher first_name: Ioan M. last_name: Pop - contributor_type: researcher first_name: Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X corr_author: '1' date_created: 2025-01-27T09:48:44Z date_published: 2025-01-27T00:00:00Z date_updated: 2026-05-20T06:34:50Z day: '27' ddc: - '530' department: - _id: GeKa - _id: GradSch doi: 10.15479/AT:ISTA:18886 file: - access_level: open_access checksum: 977dffed4bec3c7d6315aa1cbd19e8a7 content_type: text/plain creator: arashid date_created: 2025-01-27T11:27:30Z date_updated: 2025-01-27T11:27:30Z file_id: '18893' file_name: readme.txt file_size: 1017 relation: main_file success: 1 - access_level: open_access checksum: 7ab5e3e65ddf59bbf3622ace8a0cda1c content_type: application/zip creator: arashid date_created: 2025-01-27T11:27:35Z date_updated: 2025-01-27T11:27:35Z file_id: '18894' file_name: research_data.zip file_size: 33815056 relation: main_file success: 1 file_date_updated: 2025-01-27T11:27:35Z has_accepted_license: '1' month: '01' oa: 1 oa_version: Published Version project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins publisher: Institute of Science and Technology Austria related_material: record: - id: '18144' relation: used_in_publication status: public - id: '19401' relation: used_in_publication status: public status: public title: Research data for publication 'Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors' tmp: 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) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- APC_amount: 7068 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '18892' abstract: - lang: eng text: Sick individuals often conceal their disease status to group members, thereby preventing social exclusion or aggression. Here we show by behavioural, chemical, immunological and infection load analyses that sick ant pupae instead actively emit a chemical signal that in itself is sufficient to trigger their own destruction by colony members. In our experiments, this altruistic disease-signalling was performed only by worker but not queen pupae. The lack of signalling by queen pupae did not constitute cheating behaviour, but reflected their superior immune capabilities. Worker pupae suffered from extensive pathogen replication whereas queen pupae were able to restrain their infection. Our data suggest the evolution of a finely-tuned signalling system in which it is not the induction of an individual’s immune response, but rather its failure to overcome the infection, that triggers pupal signalling for sacrifice. This demonstrates a balanced interplay between individual and social immunity that efficiently achieves whole-colony health. acknowledged_ssus: - _id: LifeSc - _id: MassSpec acknowledgement: We thank Joergen Eilenberg and Nicolai V. Meyling for the fungal strain, and the ISTA Social Immunity team, Jonghyun Park and Yuko Ulrich for ant collection. We also thank the Social Immunity team, in particular David Moreno Martínez, Tanvi Madaan, Wilfrid Jean Louis and Jessica Kirchner, for experimental and molecular support, as well as Friedrich Fochler for technical support with the chemical analysis, and the ISTA Lab Support Facility, including the mass spectrometry unit, for general and chemical laboratory support. We further thank Marco Ribezzi for advice on 13C calculations and Ernst Pittenauer for discussion of the chemical data, Chris Pull and Michael Sixt for project discussion, and the Social Immunity team for comments on the manuscript. The study was funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation Programme (No. 771402; EPIDEMICSonCHIP) to SC. article_number: '10511' article_processing_charge: Yes article_type: original author: - first_name: Erika full_name: Dawson, Erika id: 31B4E2D0-F248-11E8-B48F-1D18A9856A87 last_name: Dawson - first_name: Michaela full_name: Hönigsberger, Michaela id: 953894f3-25bd-11ec-8556-f70a9d38ef60 last_name: Hönigsberger - first_name: Niklas full_name: Kampleitner, Niklas id: 2AC57FAC-F248-11E8-B48F-1D18A9856A87 last_name: Kampleitner - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Lukas full_name: Lindorfer, Lukas id: 85f0e6d3-06b3-11ec-8982-8c5049fa4455 last_name: Lindorfer - first_name: Jennifer full_name: Robb, Jennifer id: 7bc2734a-e2c6-11ea-9824-a2ed5f0662a8 last_name: Robb - first_name: Farnaz full_name: Beikzadeh Abbasi, Farnaz id: 0344bfb9-3feb-11ee-87e9-c27edc800bcd last_name: Beikzadeh Abbasi - first_name: Florian full_name: Strahodinsky, Florian id: 979E35EE-C996-11E9-8C7C-CF13E6697425 last_name: Strahodinsky - first_name: Hanna full_name: Leitner, Hanna id: 8fc5c6f6-5903-11ec-abad-c83f046253e7 last_name: Leitner - first_name: Harikrishnan full_name: Rajendran, Harikrishnan id: 876b6b34-8ff4-11ec-97c9-8d95a7aae416 last_name: Rajendran - first_name: Thomas full_name: Schmitt, Thomas last_name: Schmitt - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Dawson E, Hönigsberger M, Kampleitner N, et al. Altruistic disease signalling in ant colonies. Nature Communications. 2025;16. doi:10.1038/s41467-025-66175-z apa: Dawson, E., Hönigsberger, M., Kampleitner, N., Grasse, A. V., Lindorfer, L., Robb, J., … Cremer, S. (2025). Altruistic disease signalling in ant colonies. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-025-66175-z chicago: Dawson, Erika, Michaela Hönigsberger, Niklas Kampleitner, Anna V Grasse, Lukas Lindorfer, Jennifer Robb, Farnaz Beikzadeh, et al. “Altruistic Disease Signalling in Ant Colonies.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-66175-z. ieee: E. Dawson et al., “Altruistic disease signalling in ant colonies,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Dawson E, Hönigsberger M, Kampleitner N, Grasse AV, Lindorfer L, Robb J, Beikzadeh F, Strahodinsky F, Leitner H, Rajendran H, Schmitt T, Cremer S. 2025. Altruistic disease signalling in ant colonies. Nature Communications. 16, 10511. mla: Dawson, Erika, et al. “Altruistic Disease Signalling in Ant Colonies.” Nature Communications, vol. 16, 10511, Springer Nature, 2025, doi:10.1038/s41467-025-66175-z. short: E. Dawson, M. Hönigsberger, N. Kampleitner, A.V. Grasse, L. Lindorfer, J. Robb, F. Beikzadeh, F. Strahodinsky, H. Leitner, H. Rajendran, T. Schmitt, S. Cremer, Nature Communications 16 (2025). corr_author: '1' date_created: 2025-01-27T11:28:05Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-06-10T08:50:53Z day: '01' ddc: - '570' department: - _id: SyCr - _id: LifeSc doi: 10.1038/s41467-025-66175-z ec_funded: 1 external_id: pmid: - '41330896' file: - access_level: open_access checksum: 06244623bb7611c636652ecbc4787889 content_type: application/pdf creator: dernst date_created: 2025-12-15T13:30:33Z date_updated: 2025-12-15T13:30:33Z file_id: '20826' file_name: 2025_NatureComm_Dawson.pdf file_size: 805323 relation: main_file success: 1 file_date_updated: 2025-12-15T13:30:33Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.02.27.582277 month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/ants-signal-deadly-infection/ record: - id: '20471' relation: research_data status: public scopus_import: '1' status: public title: Altruistic disease signalling in ant colonies tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18936' abstract: - lang: eng text: A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties—the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation—can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes. acknowledgement: "The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions that helped improve our work.\r\nFunding for this work was provided by the Wellcome Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society Research Grant (RG\\R2\\232522) to M.L." article_number: iyae191 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator citation: ama: 'Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 2025;229(2). doi:10.1093/genetics/iyae191' apa: 'Grah, R., Guet, C. C., Tkačik, G., & Lagator, M. (2025). Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyae191' chicago: 'Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” Genetics. Oxford University Press, 2025. https://doi.org/10.1093/genetics/iyae191.' ieee: 'R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms to their evolutionary consequences: a primer,” Genetics, vol. 229, no. 2. Oxford University Press, 2025.' ista: 'Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.' mla: 'Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” Genetics, vol. 229, no. 2, iyae191, Oxford University Press, 2025, doi:10.1093/genetics/iyae191.' short: R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025). corr_author: '1' date_created: 2025-01-29T08:21:35Z date_published: 2025-02-01T00:00:00Z date_updated: 2025-05-19T14:08:02Z day: '01' ddc: - '570' department: - _id: CaGu - _id: GaTk doi: 10.1093/genetics/iyae191 external_id: isi: - '001379194200001' pmid: - '39601269' file: - access_level: open_access checksum: f730e416795969449ef49d97b82ac494 content_type: application/pdf creator: dernst date_created: 2025-04-16T09:41:04Z date_updated: 2025-04-16T09:41:04Z file_id: '19580' file_name: 2025_Genetics_Grah.pdf file_size: 1511688 relation: main_file success: 1 file_date_updated: 2025-04-16T09:41:04Z has_accepted_license: '1' intvolume: ' 229' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Genetics publication_identifier: eissn: - 1943-2631 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Linking molecular mechanisms to their evolutionary consequences: a primer' tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 229 year: '2025' ... --- OA_type: closed access _id: '18960' abstract: - lang: eng text: The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter. acknowledgement: We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288. article_number: a041653 article_processing_charge: No article_type: original author: - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: 'Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 2025;17(4). doi:10.1101/cshperspect.a041653' apa: 'Brückner, D., & Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a041653' chicago: 'Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory Press, 2025. https://doi.org/10.1101/cshperspect.a041653.' ieee: 'D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” Cold Spring Harbor Perspectives in Biology, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.' ista: 'Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653.' mla: 'Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives in Biology, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:10.1101/cshperspect.a041653.' short: D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025). corr_author: '1' date_created: 2025-01-29T13:33:47Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-12-30T07:08:34Z day: '01' department: - _id: EdHa doi: 10.1101/cshperspect.a041653 ec_funded: 1 external_id: isi: - '001456660400001' pmid: - '38951023' intvolume: ' 17' isi: 1 issue: '4' language: - iso: eng month: '04' oa_version: None pmid: 1 project: - _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b grant_number: ALTF 343-2022 name: A mechano-chemical theory for stem cell fate decisions in organoid development - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis publication: Cold Spring Harbor Perspectives in Biology publication_identifier: issn: - 1943-0264 publication_status: published publisher: Cold Spring Harbor Laboratory Press quality_controlled: '1' scopus_import: '1' status: public title: 'Tissue active matter: Integrating mechanics and signaling into dynamical models' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2025' ... --- OA_place: publisher _id: '18979' abstract: - lang: eng text: "Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA.\r\n\r\nThe first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue.\r\n\r\nThe aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor.\r\n\r\nWe describe a construction of a chromatic alpha complex, which enables efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline.\r\n\r\nThe second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory.\r\n\r\nIn the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot." acknowledgement: "The research presented in this thesis was funded with the Wittgenstein Prize,\r\nAustrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ondrej full_name: Draganov, Ondrej id: 2B23F01E-F248-11E8-B48F-1D18A9856A87 last_name: Draganov orcid: 0000-0003-0464-3823 citation: ama: Draganov O. Structures and computations in topological data analysis. 2025. doi:10.15479/at:ista:18979 apa: Draganov, O. (2025). Structures and computations in topological data analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18979 chicago: Draganov, Ondrej. “Structures and Computations in Topological Data Analysis.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18979. ieee: O. Draganov, “Structures and computations in topological data analysis,” Institute of Science and Technology Austria, 2025. ista: Draganov O. 2025. Structures and computations in topological data analysis. Institute of Science and Technology Austria. mla: Draganov, Ondrej. Structures and Computations in Topological Data Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18979. short: O. Draganov, Structures and Computations in Topological Data Analysis, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-01-31T17:04:40Z date_published: 2025-02-03T00:00:00Z date_updated: 2026-04-07T11:47:30Z day: '03' ddc: - '514' - '004' degree_awarded: PhD department: - _id: GradSch - _id: HeEd doi: 10.15479/at:ista:18979 file: - access_level: closed checksum: af6567e5d35e5eb330b8925ae37f1998 content_type: application/zip creator: odragano date_created: 2025-01-31T16:58:30Z date_updated: 2025-01-31T16:58:30Z file_id: '18983' file_name: Thesis.zip file_size: 11899491 relation: source_file - access_level: open_access checksum: c3fef68e35b9dc2020b2ca6006da6343 content_type: application/pdf creator: odragano date_created: 2025-02-04T16:22:07Z date_updated: 2025-02-04T16:22:07Z file_id: '19000' file_name: Thesis.pdf file_size: 8857514 relation: main_file file_date_updated: 2025-02-04T16:22:07Z has_accepted_license: '1' keyword: - topological data analysis - chromatic point set - alpha complex - persistent homology - six pack - sheaf - microlocal discrete Morse - injective resolution - collapse - knot - discrete Morse theory language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '140' project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: Mathematics, Computer Science publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15091' relation: part_of_dissertation status: public - id: '18981' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Structures and computations in topological data analysis tmp: 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) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '18984' abstract: - lang: eng text: Although planets have been found orbiting binary systems, whether they can survive binary interactions is debated. While the tightest-orbit binaries should host the most dynamically stable and long-lived circumbinary planetary systems, they are also the systems that are expected to experience mass transfer, common envelope evolution, or stellar mergers. In this study, we explore the effect of stable non-conservative mass transfer on the dynamical evolution of circumbinary planets. We present a new script that seamlessly integrates binary evolution data from the 1D binary stellar evolution code MESA into the N-body simulation code REBOUND. This integration framework enables a comprehensive examination of the dynamical evolution of circumbinary planets orbiting mass-transferring binaries, while simultaneously accounting for the detailed stellar structure evolution. In addition, we introduce a recalibration method to mitigate numerical errors from updates of binary properties during the system's dynamical evolution. We construct a reference binary model in which a 2.21M⊙ star loses its hydrogen-rich envelope through non-conservative mass transfer to the 1.76M⊙ companion star, creating a 0.38M⊙ subdwarf. We find the tightest stable orbital separation for circumbinary planets to be ≃2.5 times the binary separation after mass transfer. Accounting for tides by using the interior stellar structure, we find that tidal effects become apparent after the rapid mass transfer phase and start to fade away during the latter stage of the slow mass transfer phase. Our research provides a new framework for exploring circumbinary planet dynamics in interacting binary systems. acknowledgement: We thank the participants of the 2023 Kavli Summer Program in Astrophysics, hosted by the Max Planck Institute for Astrophysics and funded by the Kavli Foundation. In particular, Holly Preece, Selma de Mink, and Stephen Justham for their feedback and comments on our work. ZX acknowledges support from the China Scholarship Council (CSC). ST acknowledges the funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 101034413. AAT acknowledges support from the Horizon Europe research and innovation programmes under the Marie Skłodowska-Curie grant agreement no. 101103134. article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Zepei full_name: Xing, Zepei last_name: Xing - first_name: Santiago full_name: Torres Rodriguez, Santiago id: a8df4360-4328-11ee-8f1a-e502d0c83fc2 last_name: Torres Rodriguez orcid: 0000-0002-3150-8988 - first_name: Ylva Louise Linsdotter full_name: Götberg, Ylva Louise Linsdotter id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d last_name: Götberg orcid: 0000-0002-6960-6911 - first_name: Alessandro A. full_name: Trani, Alessandro A. last_name: Trani - first_name: Valeriya full_name: Korol, Valeriya last_name: Korol - first_name: Jorge full_name: Cuadra, Jorge last_name: Cuadra citation: ama: 'Xing Z, Torres Rodriguez S, Götberg YLL, Trani AA, Korol V, Cuadra J. Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries. Monthly Notices of the Royal Astronomical Society. 2025;537(1):285-292. doi:10.1093/mnras/stae2820' apa: 'Xing, Z., Torres Rodriguez, S., Götberg, Y. L. L., Trani, A. A., Korol, V., & Cuadra, J. (2025). Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae2820' chicago: 'Xing, Zepei, Santiago Torres Rodriguez, Ylva Louise Linsdotter Götberg, Alessandro A. Trani, Valeriya Korol, and Jorge Cuadra. “Combining REBOUND and MESA: Dynamical Evolution of Planets Orbiting Interacting Binaries.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2025. https://doi.org/10.1093/mnras/stae2820.' ieee: 'Z. Xing, S. Torres Rodriguez, Y. L. L. Götberg, A. A. Trani, V. Korol, and J. Cuadra, “Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries,” Monthly Notices of the Royal Astronomical Society, vol. 537, no. 1. Oxford University Press, pp. 285–292, 2025.' ista: 'Xing Z, Torres Rodriguez S, Götberg YLL, Trani AA, Korol V, Cuadra J. 2025. Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries. Monthly Notices of the Royal Astronomical Society. 537(1), 285–292.' mla: 'Xing, Zepei, et al. “Combining REBOUND and MESA: Dynamical Evolution of Planets Orbiting Interacting Binaries.” Monthly Notices of the Royal Astronomical Society, vol. 537, no. 1, Oxford University Press, 2025, pp. 285–92, doi:10.1093/mnras/stae2820.' short: Z. Xing, S. Torres Rodriguez, Y.L.L. Götberg, A.A. Trani, V. Korol, J. Cuadra, Monthly Notices of the Royal Astronomical Society 537 (2025) 285–292. date_created: 2025-02-02T23:01:53Z date_published: 2025-02-01T00:00:00Z date_updated: 2025-12-30T07:25:37Z day: '01' ddc: - '520' department: - _id: YlGo - _id: LiBu doi: 10.1093/mnras/stae2820 ec_funded: 1 external_id: arxiv: - '2410.19695' isi: - '001400731500001' file: - access_level: open_access checksum: 49fb4fe69f487d36169ccea60acbeccc content_type: application/pdf creator: dernst date_created: 2025-12-30T07:24:34Z date_updated: 2025-12-30T07:24:34Z file_id: '20881' file_name: 2025_MonthlyNoticesRAS_Xing.pdf file_size: 2974244 relation: main_file success: 1 file_date_updated: 2025-12-30T07:24:34Z has_accepted_license: '1' intvolume: ' 537' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 285-292 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries' tmp: 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) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 537 year: '2025' ...