--- OA_place: publisher OA_type: hybrid _id: '18764' abstract: - lang: eng text: We prove that a class of weakly perturbed Hamiltonians of the form H_λ= H_0 + λW, with W being a Wigner matrix, exhibits prethermalization. That is, the time evolution generated by H_λ relaxes to its ultimate thermal state via an intermediate prethermal state with a lifetime of order λ^{-2}. Moreover, we obtain a general relaxation formula, expressing the perturbed dynamics via the unperturbed dynamics and the ultimate thermal state. The proof relies on a two-resolvent law for the deformed Wigner matrix H_λ. acknowledgement: "All authors were supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nJ.R. was additionally supported by the ERC Advanced Grant “LDRaM” No. 884584.\r\nWe thank Peter Reimann and Lennart Dabelow for helpful comments. Open access funding provided by Institute of Science and Technology (IST Austria)." article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Jana full_name: Reker, Jana id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9 last_name: Reker - first_name: Volodymyr full_name: Riabov, Volodymyr id: 1949f904-edfb-11eb-afb5-e2dfddabb93b last_name: Riabov citation: ama: Erdös L, Henheik SJ, Reker J, Riabov V. Prethermalization for deformed Wigner matrices. Annales Henri Poincare. 2025;26:1991-2033. doi:10.1007/s00023-024-01518-y apa: Erdös, L., Henheik, S. J., Reker, J., & Riabov, V. (2025). Prethermalization for deformed Wigner matrices. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-024-01518-y chicago: Erdös, László, Sven Joscha Henheik, Jana Reker, and Volodymyr Riabov. “Prethermalization for Deformed Wigner Matrices.” Annales Henri Poincare. Springer Nature, 2025. https://doi.org/10.1007/s00023-024-01518-y. ieee: L. Erdös, S. J. Henheik, J. Reker, and V. Riabov, “Prethermalization for deformed Wigner matrices,” Annales Henri Poincare, vol. 26. Springer Nature, pp. 1991–2033, 2025. ista: Erdös L, Henheik SJ, Reker J, Riabov V. 2025. Prethermalization for deformed Wigner matrices. Annales Henri Poincare. 26, 1991–2033. mla: Erdös, László, et al. “Prethermalization for Deformed Wigner Matrices.” Annales Henri Poincare, vol. 26, Springer Nature, 2025, pp. 1991–2033, doi:10.1007/s00023-024-01518-y. short: L. Erdös, S.J. Henheik, J. Reker, V. Riabov, Annales Henri Poincare 26 (2025) 1991–2033. corr_author: '1' date_created: 2025-01-05T23:01:59Z date_published: 2025-06-01T00:00:00Z date_updated: 2026-04-07T12:37:11Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00023-024-01518-y ec_funded: 1 external_id: arxiv: - '2310.06677' isi: - '001385326500001' file: - access_level: open_access checksum: 49e6a934db540206f7eaa0c798553ded content_type: application/pdf creator: dernst date_created: 2025-06-25T05:38:34Z date_updated: 2025-06-25T05:38:34Z file_id: '19895' file_name: 2025_AnnalesHenriPoincare_Erdoes.pdf file_size: 977773 relation: main_file success: 1 file_date_updated: 2025-06-25T05:38:34Z has_accepted_license: '1' intvolume: ' 26' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1991-2033 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '17174' relation: earlier_version status: public - id: '20575' relation: dissertation_contains status: public - id: '19540' relation: dissertation_contains status: public scopus_import: '1' status: public title: Prethermalization for deformed Wigner matrices 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 26 year: '2025' ... --- OA_type: closed access _id: '18765' abstract: - lang: eng text: Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution. acknowledged_ssus: - _id: Bio acknowledgement: 'We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.' alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: 'Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. Lineage Tracing. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7' apa: 'Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7' chicago: 'Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.' ieee: 'G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in Lineage Tracing, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.' ista: 'Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.' mla: Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7. short: G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151. corr_author: '1' date_created: 2025-01-07T08:36:47Z date_published: 2025-01-03T00:00:00Z date_updated: 2025-04-14T07:43:46Z day: '03' department: - _id: SiHi doi: 10.1007/978-1-0716-4310-5_7 ec_funded: 1 editor: - first_name: Jorge full_name: Garcia-Marques, Jorge last_name: Garcia-Marques - first_name: Tzumin full_name: Lee, Tzumin last_name: Lee external_id: pmid: - '39745639' intvolume: ' 2886' language: - iso: eng month: '01' oa_version: None page: 139-151 place: New York, NY pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Lineage Tracing publication_identifier: eisbn: - '9781071643105' eissn: - 1940-6029 isbn: - '9781071643099' issn: - 1064-3745 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM) type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2886 year: '2025' ... --- APC_amount: 12348 EUR OA_place: publisher OA_type: hybrid _id: '18778' abstract: - lang: eng text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression. acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp - _id: PreCl acknowledgement: We thank the members of the Bernecky laboratory for helpful discussions and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade (Max Perutz Laboratories and Medical University of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This research was further supported by the Scientific Service Units of ISTA through resources provided by the Laboratory Support Facility, Electron Microscopy Facility, Scientific Computing and the Preclinical Facility. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Katarina full_name: Tluckova, Katarina id: 4AC7D980-F248-11E8-B48F-1D18A9856A87 last_name: Tluckova - first_name: Beata M full_name: Kaczmarek, Beata M id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarek - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 citation: ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7 apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7 chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7. ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” Nature Structural & Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025. ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. 32, 607–612. mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32, Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7. short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural & Molecular Biology 32 (2025) 607–612. corr_author: '1' date_created: 2025-01-08T11:20:20Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-11-20T10:28:36Z day: '01' ddc: - '570' department: - _id: CaBe doi: 10.1038/s41594-024-01448-7 external_id: isi: - '001390268000001' pmid: - '39762629' file: - access_level: open_access checksum: 2919b30b271f395888e880076a680d73 content_type: application/pdf creator: dernst date_created: 2025-04-16T08:17:27Z date_updated: 2025-04-16T08:17:27Z file_id: '19573' file_name: 2025_NatureStrucMolBiol_Tluckova.pdf file_size: 9306639 relation: main_file success: 1 file_date_updated: 2025-04-16T08:17:27Z has_accepted_license: '1' intvolume: ' 32' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 607-612 pmid: 1 project: - _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30 grant_number: P34185 name: Regulation of mammalian transcription by noncoding RNA publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14644' relation: earlier_version status: public scopus_import: '1' status: public title: Mechanism of mammalian transcriptional repression by noncoding RNA 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: 32 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18807' abstract: - lang: eng text: Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues. acknowledgement: We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: David full_name: Brückner, David id: e1e86031-6537-11eb-953a-f7ab92be508d last_name: Brückner orcid: 0000-0001-7205-2975 - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Martina full_name: Greunz, Martina id: 48A59534-F248-11E8-B48F-1D18A9856A87 last_name: Greunz - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 2025;60(4):567-580. doi:10.1016/j.devcel.2024.10.024 apa: Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., & Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.10.024 chicago: Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell. Elsevier, 2025. https://doi.org/10.1016/j.devcel.2024.10.024. ieee: S. Rus et al., “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” Developmental Cell, vol. 60, no. 4. Elsevier, pp. 567–580, 2025. ista: Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580. mla: Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:10.1016/j.devcel.2024.10.024. short: S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580. corr_author: '1' date_created: 2025-01-09T11:25:47Z date_published: 2025-02-24T00:00:00Z date_updated: 2026-06-21T22:31:16Z day: '24' ddc: - '570' department: - _id: AnKi - _id: EdHa - _id: NanoFab doi: 10.1016/j.devcel.2024.10.024 external_id: isi: - '001434279000001' pmid: - '39603235' file: - access_level: open_access checksum: bb58db4a908a1f4aabe4004706154541 content_type: application/pdf creator: dernst date_created: 2025-04-16T10:54:07Z date_updated: 2025-04-16T10:54:07Z file_id: '19584' file_name: 2025_DevelopmentalCell_Lehr.pdf file_size: 6994499 relation: main_file success: 1 file_date_updated: 2025-04-16T10:54:07Z has_accepted_license: '1' intvolume: ' 60' isi: 1 issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 567-580 pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F7802 name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public scopus_import: '1' status: public title: Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling 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: 60 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18820' abstract: - lang: eng text: 'Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy.' acknowledgement: The authors thank Dr. Matteo Carli for providing the CLN025 replica exchange MD trajectory and Matteo Allione for the fruitful discussions connected with the idea of the linear scaling estimator. This work was partially funded by NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial support by the region Friuli Venezia Giulia (project F53C22001770002 received by A.L.). article_number: '270' article_processing_charge: Yes article_type: original author: - first_name: Romina full_name: Wild, Romina last_name: Wild - first_name: Felix full_name: Wodaczek, Felix id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e last_name: Wodaczek orcid: 0009-0000-1457-795X - first_name: Vittorio full_name: Del Tatto, Vittorio last_name: Del Tatto - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alessandro full_name: Laio, Alessandro last_name: Laio citation: ama: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 2025;16. doi:10.1038/s41467-024-55449-7 apa: Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., & Laio, A. (2025). Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55449-7 chicago: Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55449-7. ieee: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance,” Nature Communications, vol. 16. Springer Nature, 2025. ista: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 16, 270. mla: Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” Nature Communications, vol. 16, 270, Springer Nature, 2025, doi:10.1038/s41467-024-55449-7. short: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025). date_created: 2025-01-12T23:04:00Z date_published: 2025-01-02T00:00:00Z date_updated: 2025-02-27T12:41:25Z day: '02' ddc: - '570' department: - _id: AnSa - _id: BiCh doi: 10.1038/s41467-024-55449-7 external_id: isi: - '001389959100009' pmid: - '39747013' file: - access_level: open_access checksum: b3d0f3568d9a87c494cf231a5324029a content_type: application/pdf creator: dernst date_created: 2025-01-14T06:59:25Z date_updated: 2025-01-14T06:59:25Z file_id: '18846' file_name: 2025_NatureComm_Wild.pdf file_size: 1216738 relation: main_file success: 1 file_date_updated: 2025-01-14T06:59:25Z has_accepted_license: '1' intvolume: ' 16' isi: 1 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: Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance 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: 16 year: '2025' ... --- OA_place: repository OA_type: green _id: '18821' abstract: - lang: eng text: 'Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.' acknowledgement: We thank J. Cremon and J. Bjerlin for earlier contributions to the configuration-interaction calculations used in this work (see Refs. [49,50]). F.B. and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter, and Lila Chergui. We further want to thank Lila Chergui for helpful comments on the paper. This research was financially supported by the Knut and Alice Wallenberg Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No. 2022-03654 VR). article_number: '013303' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Fabian full_name: Brauneis, Fabian last_name: Brauneis - first_name: Hans Werner full_name: Hammer, Hans Werner last_name: Hammer - first_name: Stephanie M. full_name: Reimann, Stephanie M. last_name: Reimann - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 2025;111(1). doi:10.1103/PhysRevA.111.013303 apa: Brauneis, F., Hammer, H. W., Reimann, S. M., & Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.111.013303 chicago: Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” Physical Review A. American Physical Society, 2025. https://doi.org/10.1103/PhysRevA.111.013303. ieee: F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of renormalized interactions using one-dimensional few-body systems as a testbed,” Physical Review A, vol. 111, no. 1. American Physical Society, 2025. ista: Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 111(1), 013303. mla: Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” Physical Review A, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:10.1103/PhysRevA.111.013303. short: F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025). date_created: 2025-01-12T23:04:00Z date_published: 2025-01-03T00:00:00Z date_updated: 2025-02-27T12:41:58Z day: '03' department: - _id: MiLe doi: 10.1103/PhysRevA.111.013303 external_id: arxiv: - '2408.10052' isi: - '001398791400004' intvolume: ' 111' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2408.10052' month: '01' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Comparison of renormalized interactions using one-dimensional few-body systems as a testbed type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18822' abstract: - lang: eng text: Let N(X) be the number of integral zeros (mathematical equation). Works of Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead a natural large sieve inequality, we recover the same bound on N(X). This is part of a more general statement, for diagonal cubic forms in (mathematical equation) variables, where we allow approximations to Hasse–Weil L-functions. acknowledgement: I thank Peter Sarnak for suggesting projects that ultimately led to the present paper. I also thank him for many encouraging discussions, helpful comments, and references. Thanks also to Tim Browning, Trevor Wooley, and Nina Zubrilina for helpful comments, and to Levent Alpöge and Will Sawin for some interesting old discussions. I thank Yang Liu, Evan O'Dorney, Ashwin Sah, and Mark Sellke for conversations illuminating the combinatorics of an older, counting version of the present Lemma 4.9. Finally, special thanks are due to the editors and referees for their patience and help with the exposition. This work was partially supported by NSF Grant DMS-1802211, and the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413. article_number: e70008 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Victor full_name: Wang, Victor id: 76096395-aea4-11ed-a680-ab8ebbd3f1b9 last_name: Wang orcid: 0000-0002-0704-7026 citation: ama: Wang V. Diagonal cubic forms and the large sieve. Mathematika. 2025;71(1). doi:10.1112/mtk.70008 apa: Wang, V. (2025). Diagonal cubic forms and the large sieve. Mathematika. London Mathematical Society. https://doi.org/10.1112/mtk.70008 chicago: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” Mathematika. London Mathematical Society, 2025. https://doi.org/10.1112/mtk.70008. ieee: V. Wang, “Diagonal cubic forms and the large sieve,” Mathematika, vol. 71, no. 1. London Mathematical Society, 2025. ista: Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1), e70008. mla: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” Mathematika, vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:10.1112/mtk.70008. short: V. Wang, Mathematika 71 (2025). corr_author: '1' date_created: 2025-01-12T23:04:01Z date_published: 2025-01-02T00:00:00Z date_updated: 2025-04-14T07:54:56Z day: '02' ddc: - '510' department: - _id: TiBr doi: 10.1112/mtk.70008 ec_funded: 1 external_id: isi: - '001388255500001' file: - access_level: open_access checksum: 700a8596b4bffce2320d074120962c22 content_type: application/pdf creator: dernst date_created: 2025-01-14T06:52:09Z date_updated: 2025-01-14T06:52:09Z file_id: '18845' file_name: 2025_Mathematika_Wang.pdf file_size: 309893 relation: main_file success: 1 file_date_updated: 2025-01-14T06:52:09Z has_accepted_license: '1' intvolume: ' 71' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Mathematika publication_identifier: eissn: - 2041-7942 issn: - 0025-5793 publication_status: published publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Diagonal cubic forms and the large sieve 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: 71 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18823' article_number: kiae651 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dechang full_name: Cao, Dechang last_name: Cao - first_name: Joke G full_name: De Jaeger-Braet, Joke G id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5 last_name: De Jaeger-Braet citation: ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 2025;197(1). doi:10.1093/plphys/kiae651' apa: 'Cao, D., & De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiae651' chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” Plant Physiology. Oxford University Press, 2025. https://doi.org/10.1093/plphys/kiae651.' ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation alterations across generations,” Plant Physiology, vol. 197, no. 1. Oxford University Press, 2025.' ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.' mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” Plant Physiology, vol. 197, no. 1, kiae651, Oxford University Press, 2025, doi:10.1093/plphys/kiae651.' short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025). corr_author: '1' date_created: 2025-01-12T23:04:02Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-07-15T08:18:19Z day: '01' ddc: - '580' department: - _id: XiFe doi: 10.1093/plphys/kiae651 external_id: isi: - '001382979900001' pmid: - '39691053' file: - access_level: open_access checksum: a9b2a12d7bc6174f27e28413e9c77a9c content_type: application/pdf creator: dernst date_created: 2025-07-15T08:17:25Z date_updated: 2025-07-15T08:17:25Z file_id: '20023' file_name: 2025_PlantPhysiology_Cao.pdf file_size: 1214018 relation: main_file success: 1 file_date_updated: 2025-07-15T08:17:25Z has_accepted_license: '1' intvolume: ' 197' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Memory of maternal temperatures: DNA methylation alterations across generations' 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: 197 year: '2025' ... --- _id: '18837' abstract: - lang: eng text: Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. article_processing_charge: No author: - 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: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger citation: ama: Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution expansion microscopy in plant roots.” 2025. doi:10.15479/AT:ISTA:18837 apa: Danzl, J. G., & Kreuzinger, C. (2025). Research Data for the publication “Super-resolution expansion microscopy in plant roots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18837 chicago: Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication ‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18837. ieee: J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution expansion microscopy in plant roots.’” Institute of Science and Technology Austria, 2025. ista: Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution expansion microscopy in plant roots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18837. mla: Danzl, Johann G., and Caroline Kreuzinger. Research Data for the Publication “Super-Resolution Expansion Microscopy in Plant Roots.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:18837. short: J.G. Danzl, C. Kreuzinger, (2025). contributor: - contributor_type: researcher first_name: Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - contributor_type: researcher first_name: Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - contributor_type: researcher first_name: Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - contributor_type: researcher first_name: Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella - contributor_type: researcher first_name: Vitali id: 7e146587-8972-11ed-ae7b-d7a32ea86a81 last_name: Vistunou - contributor_type: researcher first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - contributor_type: researcher first_name: Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - contributor_type: researcher first_name: Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - contributor_type: researcher first_name: Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer - contributor_type: researcher first_name: Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - contributor_type: researcher first_name: Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - contributor_type: researcher first_name: Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - contributor_type: researcher first_name: Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - contributor_type: researcher first_name: Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - contributor_type: researcher first_name: Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 corr_author: '1' date_created: 2025-01-13T09:51:29Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-06-10T08:30:20Z department: - _id: JoDa doi: 10.15479/AT:ISTA:18837 file: - access_level: open_access checksum: a522d476ca1106163abb403ee156f6d0 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:09:15Z date_updated: 2025-03-07T10:09:15Z file_id: '19312' file_name: Fig 1D+2D PlantEx.tif file_size: 588707932 relation: main_file success: 1 - access_level: open_access checksum: 2d0e8279e85821de946fa8dbc4ed8134 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:29:22Z date_updated: 2025-03-07T10:29:22Z file_id: '19313' file_name: Fig 1D+2D Pre-expansion.tif file_size: 786998434 relation: main_file success: 1 - access_level: open_access checksum: 9b965e160fb7ec9900606994fe0c3045 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:31:59Z date_updated: 2025-03-07T10:31:59Z file_id: '19314' file_name: Fig 1E PlantEx.tif file_size: 108411 relation: main_file success: 1 - access_level: open_access checksum: 38857ce7d0b8c4b71937ca60eef539b3 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:32:02Z date_updated: 2025-03-07T10:32:02Z file_id: '19315' file_name: Fig 1E Pre-expansion.tif file_size: 114825 relation: main_file success: 1 - access_level: open_access checksum: fbadff70783e9c045df7aba7b5b2087c content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:32:06Z date_updated: 2025-03-07T10:32:06Z file_id: '19316' file_name: Fig 1G PlantEx.tif file_size: 1816371 relation: main_file success: 1 - access_level: open_access checksum: d240605f1c2d94da98e5205725ce0d9a content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:32:16Z date_updated: 2025-03-07T10:32:16Z file_id: '19317' file_name: Fig 1G Pre-expansion.tif file_size: 915960 relation: main_file success: 1 - access_level: open_access checksum: fe491eaccfe4adef56fa26c078060f00 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:32:22Z date_updated: 2025-03-07T10:32:22Z file_id: '19318' file_name: Fig 1H PlantEx.tif file_size: 766038 relation: main_file success: 1 - access_level: open_access checksum: 58b7bdd4588ae8548e802a71b3d25106 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:32:27Z date_updated: 2025-03-07T10:32:27Z file_id: '19319' file_name: Fig 1H Pre-expansion.tif file_size: 783535 relation: main_file success: 1 - 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access_level: open_access checksum: 02e32d2cf4b6aa0491b36f3b1b404517 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T11:08:49Z date_updated: 2025-03-07T11:08:49Z file_id: '19360' file_name: SF8_2.tif file_size: 6768975 relation: main_file success: 1 - access_level: open_access checksum: f6ad4696fb9f702d4d7a5411aefa87da content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T11:09:01Z date_updated: 2025-03-07T11:09:01Z file_id: '19361' file_name: SF8_3.tif file_size: 6768975 relation: main_file success: 1 - access_level: open_access checksum: 55580709fd705702a590ebbeb0e0f918 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T11:09:13Z date_updated: 2025-03-07T11:09:13Z file_id: '19362' file_name: SF8_4.tif file_size: 6768975 relation: main_file success: 1 file_date_updated: 2025-03-07T11:09:13Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '19003' relation: used_in_publication status: public status: public title: Research Data for the publication "Super-resolution expansion microscopy in plant roots" 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- 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 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_place: publisher _id: '18871' abstract: - lang: eng text: "\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n" acknowledged_ssus: - _id: SSU - _id: M-Shop - _id: NanoFab acknowledgement: "This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 citation: ama: Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:10.15479/at:ista:18871 apa: Arnold, G. M. (2025). Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18871 chicago: Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18871. ieee: G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025. ista: Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria. mla: Arnold, Georg M. Microwave-Optic Interconnects for Superconducting Circuits. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18871. short: G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-01-24T10:28:39Z date_published: 2025-01-24T00:00:00Z date_updated: 2026-04-16T12:20:43Z day: '24' ddc: - '530' degree_awarded: PhD department: - _id: JoFi - _id: GradSch doi: 10.15479/at:ista:18871 ec_funded: 1 file: - access_level: closed checksum: 71872702e8f46c275eaea44efc4d304f content_type: application/x-zip-compressed creator: cchlebak date_created: 2025-01-29T08:38:08Z date_updated: 2026-01-29T23:30:03Z embargo_to: open_access file_id: '18946' file_name: tex for upload.zip file_size: 18856130 relation: source_file - access_level: open_access checksum: dfaa06591970f4bff163705802fad56d content_type: application/pdf creator: cchlebak date_created: 2025-01-29T08:38:34Z date_updated: 2026-01-29T23:30:03Z embargo: 2026-01-29 file_id: '18947' file_name: ISTThesisGA2022_final.pdf file_size: 17344760 relation: main_file file_date_updated: 2026-01-29T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '135' project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: 2671EB66-B435-11E9-9278-68D0E5697425 name: Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6609' relation: part_of_dissertation status: public - id: '8529' relation: part_of_dissertation status: public - id: '18953' relation: part_of_dissertation status: public - id: '10924' relation: part_of_dissertation status: public - id: '9114' relation: part_of_dissertation status: public - id: '13200' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Microwave-optic interconnects for superconducting circuits tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 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' ...