--- OA_place: publisher _id: '20203' abstract: - lang: eng text: Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon. acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: EM-Fac - _id: LifeSc - _id: ScienComp acknowledgement: "The project in Chapter 2 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 3 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 4 has received financing from the European Research Council grant\r\nagreement No. 949120 under the European Union’s Horizon 2020 research and innovation\r\nprogramme. The Analytical Instrumentation Center of the TU Wien acknowledges support by\r\nthe FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state\r\nof Lower Austria and the European Regional Development Fund under grant no. WST3-F542638/004-2021.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Juan Carlos A full_name: Sobarzo Ponce, Juan Carlos A id: 4B807D68-AE37-11E9-AC72-31CAE5697425 last_name: Sobarzo Ponce citation: ama: 'Sobarzo Ponce JCA. Tribocharging of identical insulators : Triboelectric series, triboelectric cycles and surface charges. 2025. doi:10.15479/AT-ISTA-20203' apa: 'Sobarzo Ponce, J. C. A. (2025). Tribocharging of identical insulators : Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20203' chicago: 'Sobarzo Ponce, Juan Carlos A. “Tribocharging of Identical Insulators : Triboelectric Series, Triboelectric Cycles and Surface Charges.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20203.' ieee: 'J. C. A. Sobarzo Ponce, “Tribocharging of identical insulators : Triboelectric series, triboelectric cycles and surface charges,” Institute of Science and Technology Austria, 2025.' ista: 'Sobarzo Ponce JCA. 2025. Tribocharging of identical insulators : Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria.' mla: 'Sobarzo Ponce, Juan Carlos A. Tribocharging of Identical Insulators : Triboelectric Series, Triboelectric Cycles and Surface Charges. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20203.' short: 'J.C.A. Sobarzo Ponce, Tribocharging of Identical Insulators : Triboelectric Series, Triboelectric Cycles and Surface Charges, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-08-21T11:42:59Z date_published: 2025-08-27T00:00:00Z date_updated: 2026-04-28T13:44:56Z day: '27' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-20203 ec_funded: 1 file: - access_level: open_access checksum: 661b9d3786cfc985be811befc3262bf5 content_type: application/pdf creator: jsobarzo date_created: 2025-08-27T14:50:32Z date_updated: 2025-08-27T14:50:32Z file_id: '20237' file_name: 2025_Sobarzo_JuanCarlos_Thesis.pdf file_size: 12667200 relation: main_file success: 1 - access_level: closed checksum: ca2f24e6c3b55912982521707552a0f5 content_type: application/x-zip-compressed creator: jsobarzo date_created: 2025-08-27T14:50:32Z date_updated: 2025-08-28T08:19:07Z file_id: '20238' file_name: 2025_Sobarzo_JuanCarlos_Thesis.zip file_size: 18940521 relation: source_file file_date_updated: 2025-08-28T08:19:07Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '96' project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication_identifier: isbn: - 978-3-99078-062-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12109' relation: part_of_dissertation status: public - id: '15322' relation: part_of_dissertation status: public - id: '19278' relation: part_of_dissertation status: public status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 title: 'Tribocharging of identical insulators : Triboelectric series, triboelectric cycles and surface charges' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20223' abstract: - lang: eng text: The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become “sheltered” from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favor in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Muller's hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e. selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss. acknowledged_ssus: - _id: ScienComp acknowledgement: We thank Filip Ruzicka, Colin Olito, Akane Uesugi, Melissa Toups, Daniel Jeffries, the Associate Editor, and anonymous reviewers, for comments and suggestions on earlier versions of the paper. We are particularly grateful to Deborah Charlesworth and Brian Charlesworth for extensive comments on two different drafts of the manuscript. We also thank Aneil Agrawal and Thomas Lenormand for email correspondence about the data on dominance and ways to interpret it. Technical support was provided by ISTA Scientific Computing Unit. article_number: msaf177 article_processing_charge: Yes article_type: original author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Tim full_name: Connallon, Tim last_name: Connallon citation: ama: Mrnjavac A, Vicoso B, Connallon T. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 2025;42(8). doi:10.1093/molbev/msaf177 apa: Mrnjavac, A., Vicoso, B., & Connallon, T. (2025). An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msaf177 chicago: Mrnjavac, Andrea, Beatriz Vicoso, and Tim Connallon. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” Molecular Biology and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf177. ieee: A. Mrnjavac, B. Vicoso, and T. Connallon, “An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content,” Molecular Biology and Evolution, vol. 42, no. 8. Oxford University Press, 2025. ista: Mrnjavac A, Vicoso B, Connallon T. 2025. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 42(8), msaf177. mla: Mrnjavac, Andrea, et al. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” Molecular Biology and Evolution, vol. 42, no. 8, msaf177, Oxford University Press, 2025, doi:10.1093/molbev/msaf177. short: A. Mrnjavac, B. Vicoso, T. Connallon, Molecular Biology and Evolution 42 (2025). date_created: 2025-08-24T22:01:31Z date_published: 2025-08-01T00:00:00Z date_updated: 2025-09-30T14:25:57Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/molbev/msaf177 external_id: isi: - '001547617100001' pmid: - '40713898' file: - access_level: open_access checksum: f40abffa56cb1e9ff65800f2a7d7b39a content_type: application/pdf creator: dernst date_created: 2025-09-02T07:47:32Z date_updated: 2025-09-02T07:47:32Z file_id: '20274' file_name: 2025_MolecularBioEvolution_Mrnjavac.pdf file_size: 1239841 relation: main_file success: 1 file_date_updated: 2025-09-02T07:47:32Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://git.ista.ac.at/bvicoso/xydegenerate scopus_import: '1' status: public title: An extension of Muller's sheltering hypothesis for the evolution of sex chromosome gene content 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: 42 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20295' abstract: - lang: eng text: 'Scanning Kelvin probe microscopy (SKPM) is a powerful technique for macroscopic imaging of the electrostatic potential above a surface. Though most often used to image work-function variations of conductive surfaces, it can also be used to probe the surface charge on insulating surfaces. In both cases, relating the measured potential to the underlying signal is non-trivial. Here, general relationships are derived between the measured SKPM voltage and the underlying source, revealing either can be cast as a convolution with an appropriately scaled point spread function (PSF). For charge that exists on a thin insulating layer above a conductor, the PSF has the same shape as what would occur from a work-function variation alone, differing by a simple scaling factor. This relationship is confirmed by: (1) backing it out from finite-element simulations of work-function and charge signals, and (2) experimentally comparing the measured PSF from a small work-function target to that from a small charge spot. This scaling factor is further validated by comparing SKPM charge measurements with Faraday cup measurements for highly charged samples from contact-charging experiments. These results highlight a heretofore unappreciated connection between SKPM voltage and charge signals, offering a rigorous recipe to extract either from experimental data.' acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: ScienComp - _id: LifeSc acknowledgement: This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing Facility, and Lab Support Facility. The authors wish to thank Dmytro Rak and Juan Carlos Sobarzo for letting us use their equipment. The authors wish to thank Evgeniia Volobueva for advice in preparing PFIB samples. The authors wish to thank the contributions of the whole Waitukaitis group for useful discussions and feedback. article_number: e00521 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Felix full_name: Pertl, Felix id: 6313aec0-15b2-11ec-abd3-ed67d16139af last_name: Pertl orcid: 0000-0003-0463-5794 - first_name: Lubuna B full_name: Shafeek, Lubuna B id: 3CD37A82-F248-11E8-B48F-1D18A9856A87 last_name: Shafeek orcid: 0000-0001-7180-6050 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. A duality between surface charge and work function in scanning Kelvin probe microscopy. Advanced Materials Interfaces. 2025;12(19). doi:10.1002/admi.202500521 apa: Lenton, I. C., Pertl, F., Shafeek, L. B., & Waitukaitis, S. R. (2025). A duality between surface charge and work function in scanning Kelvin probe microscopy. Advanced Materials Interfaces. Wiley. https://doi.org/10.1002/admi.202500521 chicago: Lenton, Isaac C, Felix Pertl, Lubuna B Shafeek, and Scott R Waitukaitis. “A Duality between Surface Charge and Work Function in Scanning Kelvin Probe Microscopy.” Advanced Materials Interfaces. Wiley, 2025. https://doi.org/10.1002/admi.202500521. ieee: I. C. Lenton, F. Pertl, L. B. Shafeek, and S. R. Waitukaitis, “A duality between surface charge and work function in scanning Kelvin probe microscopy,” Advanced Materials Interfaces, vol. 12, no. 19. Wiley, 2025. ista: Lenton IC, Pertl F, Shafeek LB, Waitukaitis SR. 2025. A duality between surface charge and work function in scanning Kelvin probe microscopy. Advanced Materials Interfaces. 12(19), e00521. mla: Lenton, Isaac C., et al. “A Duality between Surface Charge and Work Function in Scanning Kelvin Probe Microscopy.” Advanced Materials Interfaces, vol. 12, no. 19, e00521, Wiley, 2025, doi:10.1002/admi.202500521. short: I.C. Lenton, F. Pertl, L.B. Shafeek, S.R. Waitukaitis, Advanced Materials Interfaces 12 (2025). corr_author: '1' date_created: 2025-09-07T22:01:33Z date_published: 2025-10-01T00:00:00Z date_updated: 2025-12-30T09:31:25Z day: '01' ddc: - '530' department: - _id: ScWa - _id: NanoFab doi: 10.1002/admi.202500521 ec_funded: 1 external_id: arxiv: - '2506.07187' isi: - '001560163400001' file: - access_level: open_access checksum: 906fcc7733be8ce8a83600427b82cd5a content_type: application/pdf creator: dernst date_created: 2025-12-30T09:31:11Z date_updated: 2025-12-30T09:31:11Z file_id: '20908' file_name: 2025_AdvMaterialsInterfaces_Lenton.pdf file_size: 1830117 relation: main_file success: 1 file_date_updated: 2025-12-30T09:31:11Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '19' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: Advanced Materials Interfaces publication_identifier: eissn: - 2196-7350 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: A duality between surface charge and work function in scanning Kelvin probe microscopy 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: 12 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '20296' abstract: - lang: eng text: Learning-based systems are increasingly deployed across various domains, yet the complexity of traditional neural networks poses significant challenges for formal verification. Unlike conventional neural networks, learned Logic Gate Networks (LGNs) replace multiplications with Boolean logic gates, yielding a sparse, netlist-like architecture that is inherently more amenable to symbolic verification, while still delivering promising performance. In this paper, we introduce a SAT encoding for verifying global robustness and fairness in LGNs. We evaluate our method on five benchmark datasets, including a newly constructed 5-class variant, and find that LGNs are both verification-friendly and maintain strong predictive performance. acknowledged_ssus: - _id: ScienComp acknowledgement: "This work is supported in part by the ERC grant under Grant No. ERC-2020-AdG 101020093 and\r\nthe Austrian Science Fund (FWF) [10.55776/COE12]. This research was supported by the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)." alternative_title: - PMLR article_number: '26' article_processing_charge: No arxiv: 1 author: - first_name: Fabian full_name: Kresse, Fabian id: faff3c84-23f6-11ef-9085-e5187b51c604 last_name: Kresse - first_name: Zhengqi full_name: Yu, Zhengqi id: 20aa2ae8-f2f1-11ed-bbfa-8205053f1342 last_name: Yu - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Kresse F, Yu E, Lampert C, Henzinger TA. Logic gate neural networks are good for verification. In: 2nd International Conferenceon Neuro-Symbolic Systems. Vol 288. ML Research Press; 2025.' apa: 'Kresse, F., Yu, E., Lampert, C., & Henzinger, T. A. (2025). Logic gate neural networks are good for verification. In 2nd International Conferenceon Neuro-Symbolic Systems (Vol. 288). Philadephia, PA, United States: ML Research Press.' chicago: Kresse, Fabian, Emily Yu, Christoph Lampert, and Thomas A Henzinger. “Logic Gate Neural Networks Are Good for Verification.” In 2nd International Conferenceon Neuro-Symbolic Systems, Vol. 288. ML Research Press, 2025. ieee: F. Kresse, E. Yu, C. Lampert, and T. A. Henzinger, “Logic gate neural networks are good for verification,” in 2nd International Conferenceon Neuro-Symbolic Systems, Philadephia, PA, United States, 2025, vol. 288. ista: 'Kresse F, Yu E, Lampert C, Henzinger TA. 2025. Logic gate neural networks are good for verification. 2nd International Conferenceon Neuro-Symbolic Systems. NeuS: International Conferenceon Neuro-Symbolic Systems, PMLR, vol. 288, 26.' mla: Kresse, Fabian, et al. “Logic Gate Neural Networks Are Good for Verification.” 2nd International Conferenceon Neuro-Symbolic Systems, vol. 288, 26, ML Research Press, 2025. short: F. Kresse, E. Yu, C. Lampert, T.A. Henzinger, in:, 2nd International Conferenceon Neuro-Symbolic Systems, ML Research Press, 2025. conference: end_date: 2025-05-30 location: Philadephia, PA, United States name: 'NeuS: International Conferenceon Neuro-Symbolic Systems' start_date: 2025-05-28 corr_author: '1' date_created: 2025-09-07T22:01:34Z date_published: 2025-06-01T00:00:00Z date_updated: 2025-09-09T08:12:44Z day: '01' ddc: - '000' department: - _id: ChLa - _id: ToHe ec_funded: 1 external_id: arxiv: - '2505.19932' file: - access_level: open_access checksum: 90a32defed34787e771a5c1623b6b0d2 content_type: application/pdf creator: dernst date_created: 2025-09-09T08:10:13Z date_updated: 2025-09-09T08:10:13Z file_id: '20314' file_name: 2025_NeuS_Kresse.pdf file_size: 295466 relation: main_file success: 1 file_date_updated: 2025-09-09T08:10:13Z has_accepted_license: '1' intvolume: ' 288' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 2nd International Conferenceon Neuro-Symbolic Systems publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Logic gate neural networks are good for verification type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 288 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '20319' abstract: - lang: eng text: The time needed by deep convection to bring the atmosphere back to equilibrium is called convective adjustment timescale or simply adjustment timescale, typically denoted by . In the Community Atmospheric Model|Community Atmosphere Model (CAM), is the convective available potential energy (CAPE) relaxation timescale and is 1 hr, worldwide. Observational evidence suggests that is generally longer than 1 hr. Further, continental and oceanic convection are different in terms of the vigor of updrafts and can have different longevities. So using hour worldwide in CAM has two potential caveats. A longer improves the simulation of the mean climate. However, it does not address the land‐ocean heterogeneity of atmospheric deep convection. We investigate the prescription of two different CAPE relaxation timescales for land ( hr) and ocean ( to 4 hr). It is arguably an extremely crude parameterization of boundary layer control on atmospheric convection. We contrast a suite of 5‐year‐long simulations with two different for land and ocean to having one globally. The choice of longer over ocean is guided by previous studies and inspired by observational pieces of evidence. Nonetheless, to complement our variable experiments, we perform a simulation with  hr and  hrs. Most importantly, our key findings are immune to the exact values of prescribed and . The CAM model, with two values , improves convective‐stratiform rainfall partitioning and the Madden–Julian oscillation propagation characteristics. acknowledged_ssus: - _id: ScienComp acknowledgement: The authors gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We would like to thank Prof. Courtney Schumacher and Dr. Aaron Funk of Texas A&M University for their help in understanding the TRMM Radar data. The authors are grateful to two anonymous reviewers who helped improve the quality of this paper. article_number: e2025MS005035 article_processing_charge: Yes article_type: original author: - first_name: BIDYUT B full_name: GOSWAMI, BIDYUT B id: 3a4ac09c-6d61-11ec-bf66-884cde66b64b last_name: GOSWAMI orcid: 0000-0001-8602-3083 - first_name: Andrea full_name: Polesello, Andrea id: 74c777f4-32da-11ee-b498-874db0835561 last_name: Polesello - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: ama: GOSWAMI BB, Polesello A, Muller CJ. An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6). Journal of Advances in Modeling Earth Systems. 2025;17(9). doi:10.1029/2025ms005035 apa: GOSWAMI, B. B., Polesello, A., & Muller, C. J. (2025). An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6). Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2025ms005035 chicago: GOSWAMI, BIDYUT B, Andrea Polesello, and Caroline J Muller. “An Assessment of Representing Land‐ocean Heterogeneity via CAPE Relaxation Timescale in the Community Atmospheric Model 6 (CAM6).” Journal of Advances in Modeling Earth Systems. Wiley, 2025. https://doi.org/10.1029/2025ms005035. ieee: B. B. GOSWAMI, A. Polesello, and C. J. Muller, “An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6),” Journal of Advances in Modeling Earth Systems, vol. 17, no. 9. Wiley, 2025. ista: GOSWAMI BB, Polesello A, Muller CJ. 2025. An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6). Journal of Advances in Modeling Earth Systems. 17(9), e2025MS005035. mla: GOSWAMI, BIDYUT B., et al. “An Assessment of Representing Land‐ocean Heterogeneity via CAPE Relaxation Timescale in the Community Atmospheric Model 6 (CAM6).” Journal of Advances in Modeling Earth Systems, vol. 17, no. 9, e2025MS005035, Wiley, 2025, doi:10.1029/2025ms005035. short: B.B. GOSWAMI, A. Polesello, C.J. Muller, Journal of Advances in Modeling Earth Systems 17 (2025). corr_author: '1' date_created: 2025-09-10T05:36:16Z date_published: 2025-09-01T00:00:00Z date_updated: 2025-09-10T08:14:28Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1029/2025ms005035 ec_funded: 1 file: - access_level: open_access checksum: 5961d6290432c5ac0e8587ef07f30c9b content_type: application/pdf creator: dernst date_created: 2025-09-10T08:12:34Z date_updated: 2025-09-10T08:12:34Z file_id: '20338' file_name: 2025_JAMES_Goswami.pdf file_size: 2143025 relation: main_file success: 1 file_date_updated: 2025-09-10T08:12:34Z has_accepted_license: '1' intvolume: ' 17' issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version project: - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Journal of Advances in Modeling Earth Systems publication_identifier: eissn: - 1942-2466 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: An assessment of representing land‐ocean heterogeneity via CAPE relaxation timescale in the Community Atmospheric Model 6 (CAM6) 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: 17 year: '2025' ... --- OA_place: publisher _id: '20357' acknowledged_ssus: - _id: ScienComp - _id: E-Lib acknowledgement: "I would also like to acknowledge the Austrian Academy of Sciences for funding through the\r\nDOC Fellowship program (fellowship number 26917), the Grants Office at ISTA for their\r\nassistance with the application, and the Scientific Computing Unit for their support regarding\r\nhigh-performance computation.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Natalia full_name: Ruzickova, Natalia id: D2761128-D73D-11E9-A1BF-BA0DE6697425 last_name: Ruzickova citation: ama: Ruzickova N. Effect propagation in biological networks. 2025. doi:10.15479/AT-ISTA-20357 apa: Ruzickova, N. (2025). Effect propagation in biological networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20357 chicago: Ruzickova, Natalia. “Effect Propagation in Biological Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20357. ieee: N. Ruzickova, “Effect propagation in biological networks,” Institute of Science and Technology Austria, 2025. ista: Ruzickova N. 2025. Effect propagation in biological networks. Institute of Science and Technology Austria. mla: Ruzickova, Natalia. Effect Propagation in Biological Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20357. short: N. Ruzickova, Effect Propagation in Biological Networks, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-09-15T17:04:48Z date_published: 2025-09-15T00:00:00Z date_updated: 2026-04-07T12:02:39Z day: '15' ddc: - '570' - '530' degree_awarded: PhD department: - _id: GradSch - _id: GaTk doi: 10.15479/AT-ISTA-20357 file: - access_level: closed checksum: 991e81bc16a76b4e0c352567728fd2c5 content_type: application/pdf creator: nruzicko date_created: 2025-09-16T12:56:06Z date_updated: 2025-11-27T10:00:25Z embargo: 2026-09-14 embargo_to: open_access file_id: '20360' file_name: 2025_Ruzickova_Natalia_Thesis.pdf file_size: 43518367 relation: main_file title: Effect propagation in biological networks - access_level: closed checksum: c4ab257adad116083d8a97fac69b2dde content_type: application/zip creator: nruzicko date_created: 2025-09-16T12:59:23Z date_updated: 2025-09-16T12:59:23Z file_id: '20361' file_name: 2025_Ruzickova_Natalia_Thesis_source.zip file_size: 53464789 relation: source_file file_date_updated: 2025-11-27T10:00:25Z has_accepted_license: '1' keyword: - gene regulation - networks - omnigenic model - pancreas - collective behaviour language: - iso: eng month: '09' oa_version: Published Version page: '160' project: - _id: 7bec9174-9f16-11ee-852c-ded9fe5f810e name: Collective behaviour of cells in pancreatic Islets of Langerhans publication_identifier: isbn: - 978-3-99078-066-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18525' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Effect propagation in biological networks type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20492' abstract: - lang: eng text: The glassy thermal conductivities observed in crystalline inorganic perovskites such as Cs3Bi2I6Cl3 are perplexing and lacking theoretical explanations. Here, we first experimentally measure its thermal transport behavior from 20 to 300 K, after synthesizing Cs3Bi2I6Cl3 single crystals. Using path-integral molecular dynamics simulations driven by machine learning potentials, we reveal that Cs3Bi2I6Cl3 has large lattice distortions at low temperatures, which may be related to the large atomic size mismatch. Employing the Wigner formulation of thermal transport, we reproduce theexperimental thermal conductivities based on lattice-distorted structures. This studythus provides a framework for predicting and understanding glassy thermal transportin materials with strong lattice disorder. acknowledged_ssus: - _id: ScienComp acknowledgement: Z.Z. acknowledges the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. We acknowledge the high-performance computing facilities offered by Institute of Science and Technology Austria and The University of Hong Kong. article_processing_charge: No article_type: original author: - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Zheyong full_name: Fan, Zheyong last_name: Fan - first_name: Michele full_name: Simoncelli, Michele last_name: Simoncelli - first_name: Chen full_name: Chen, Chen last_name: Chen - first_name: Ting full_name: Liang, Ting last_name: Liang - first_name: Yue full_name: Chen, Yue last_name: Chen - first_name: Geoff full_name: Thornton, Geoff last_name: Thornton - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Zeng Z, Fan Z, Simoncelli M, et al. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. 2025;122(41):e2415664122. doi:10.1073/pnas.2415664122 apa: Zeng, Z., Fan, Z., Simoncelli, M., Chen, C., Liang, T., Chen, Y., … Cheng, B. (2025). Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2415664122 chicago: Zeng, Zezhu, Zheyong Fan, Michele Simoncelli, Chen Chen, Ting Liang, Yue Chen, Geoff Thornton, and Bingqing Cheng. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2415664122. ieee: Z. Zeng et al., “Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3,” Proceedings of the National Academy of Sciences, vol. 122, no. 41. National Academy of Sciences, p. e2415664122, 2025. ista: Zeng Z, Fan Z, Simoncelli M, Chen C, Liang T, Chen Y, Thornton G, Cheng B. 2025. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. 122(41), e2415664122. mla: Zeng, Zezhu, et al. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” Proceedings of the National Academy of Sciences, vol. 122, no. 41, National Academy of Sciences, 2025, p. e2415664122, doi:10.1073/pnas.2415664122. short: Z. Zeng, Z. Fan, M. Simoncelli, C. Chen, T. Liang, Y. Chen, G. Thornton, B. Cheng, Proceedings of the National Academy of Sciences 122 (2025) e2415664122. corr_author: '1' date_created: 2025-10-19T22:01:31Z date_published: 2025-10-14T00:00:00Z date_updated: 2026-02-16T12:32:11Z day: '14' ddc: - '540' department: - _id: BiCh doi: 10.1073/pnas.2415664122 ec_funded: 1 external_id: isi: - '001600415200001' pmid: - '41052324' file: - access_level: open_access checksum: 3f9cd0d67ffe9110fb238407671584b7 content_type: application/pdf creator: dernst date_created: 2025-10-21T10:02:15Z date_updated: 2025-10-21T10:02:15Z file_id: '20513' file_name: 2025_PNAS_Zeng.pdf file_size: 12244843 relation: main_file success: 1 file_date_updated: 2025-10-21T10:02:15Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '41' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: e2415664122 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity scopus_import: '1' status: public title: Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3 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_type: closed access _id: '20704' abstract: - lang: eng text: Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES. acknowledged_ssus: - _id: ScienComp acknowledgement: P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai. article_processing_charge: No article_type: original author: - first_name: Ping full_name: Tuo, Ping id: 6e5644c0-c180-11ed-a2da-facc4c9f4f09 last_name: Tuo - first_name: Zezhu full_name: Zeng, Zezhu id: 54a2c730-803f-11ed-ab7e-95b29d2680e7 last_name: Zeng orcid: 0000-0001-5126-4928 - first_name: Jiale full_name: Chen, Jiale id: 4d0a9064-1ff6-11ee-9fa6-ec046c604785 last_name: Chen orcid: 0000-0001-5337-5875 - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 2025;21(22):11427-11435. doi:10.1021/acs.jctc.5c01248 apa: Tuo, P., Zeng, Z., Chen, J., & Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01248 chicago: Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01248. ieee: P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” Journal of Chemical Theory and Computation, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025. ista: Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435. mla: Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” Journal of Chemical Theory and Computation, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:10.1021/acs.jctc.5c01248. short: P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435. corr_author: '1' date_created: 2025-11-30T23:02:06Z date_published: 2025-10-31T00:00:00Z date_updated: 2025-12-01T15:40:27Z day: '31' department: - _id: BiCh - _id: DaAl doi: 10.1021/acs.jctc.5c01248 ec_funded: 1 external_id: isi: - '001605927900001' pmid: - '41172130' intvolume: ' 21' isi: 1 issue: '22' language: - iso: eng month: '10' oa_version: None page: 11427-11435 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/tuoping/alchemicalFES scopus_import: '1' status: public title: Scalable multitemperature free energy sampling of classical Ising spin states type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20705' abstract: - lang: eng text: Optical tweezers are widely used as a highly sensitive tool to measure forces on micron-scale particles. One such application is the measurement of the electric charge of a particle, which can be done with high precision in liquids, air, or vacuum. We experimentally investigate how the trapping laser itself can electrically charge such a particle, in our case a ∼1  μ⁢m SiO2 sphere in air. We model the charging mechanism as a two-photon process which reproduces the experimental data with high fidelity. acknowledged_ssus: - _id: M-Shop - _id: ScienComp acknowledgement: We thank Todor Asenov and Abdulhamid Baghdadi for their outstanding technical support and Dr. Michael Gleichweit and Mercede Azizbaig Mohajer for the helpful discussions. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreements No. 949120 and No. 805041) and the Swiss National Science Foundation (SNSF, Project No. 200021-236446). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop and the Scientific Computing service unit. article_number: '218202' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Andrea full_name: Stöllner, Andrea id: 4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed last_name: Stöllner orcid: 0000-0002-0464-8440 - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: James full_name: Millen, James last_name: Millen - first_name: Renjiro full_name: Shibuya, Renjiro last_name: Shibuya - first_name: Hisao full_name: Ishii, Hisao last_name: Ishii - first_name: Dmytro full_name: Rak, Dmytro id: 70313b46-47c2-11ec-9e88-cd79101918fe last_name: Rak - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 - first_name: Grégory full_name: David, Grégory last_name: David - first_name: Ruth full_name: Signorell, Ruth last_name: Signorell - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Stöllner A, Lenton IC, Volosniev A, et al. Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. 2025;135(21). doi:10.1103/5xd9-4tjj apa: Stöllner, A., Lenton, I. C., Volosniev, A., Millen, J., Shibuya, R., Ishii, H., … Waitukaitis, S. R. (2025). Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. American Physical Society. https://doi.org/10.1103/5xd9-4tjj chicago: Stöllner, Andrea, Isaac C Lenton, Artem Volosniev, James Millen, Renjiro Shibuya, Hisao Ishii, Dmytro Rak, et al. “Using Optical Tweezers to Simultaneously Trap, Charge, and Measure the Charge of a Microparticle in Air.” Physical Review Letters. American Physical Society, 2025. https://doi.org/10.1103/5xd9-4tjj. ieee: A. Stöllner et al., “Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air,” Physical Review Letters, vol. 135, no. 21. American Physical Society, 2025. ista: Stöllner A, Lenton IC, Volosniev A, Millen J, Shibuya R, Ishii H, Rak D, Alpichshev Z, David G, Signorell R, Muller CJ, Waitukaitis SR. 2025. Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air. Physical Review Letters. 135(21), 218202. mla: Stöllner, Andrea, et al. “Using Optical Tweezers to Simultaneously Trap, Charge, and Measure the Charge of a Microparticle in Air.” Physical Review Letters, vol. 135, no. 21, 218202, American Physical Society, 2025, doi:10.1103/5xd9-4tjj. short: A. Stöllner, I.C. Lenton, A. Volosniev, J. Millen, R. Shibuya, H. Ishii, D. Rak, Z. Alpichshev, G. David, R. Signorell, C.J. Muller, S.R. Waitukaitis, Physical Review Letters 135 (2025). corr_author: '1' date_created: 2025-11-30T23:02:07Z date_published: 2025-11-21T00:00:00Z date_updated: 2026-04-28T13:09:27Z day: '21' ddc: - '530' - '550' department: - _id: ZhAl - _id: CaMu - _id: ScWa doi: 10.1103/5xd9-4tjj ec_funded: 1 external_id: arxiv: - '2507.17591' file: - access_level: open_access checksum: a5f76b1230cc7b039ecd0dbd6f99e775 content_type: application/pdf creator: dernst date_created: 2025-12-01T08:19:46Z date_updated: 2025-12-01T08:19:46Z file_id: '20717' file_name: 2025_PhysReviewLetters_Stoellner.pdf file_size: 1761373 relation: main_file success: 1 file_date_updated: 2025-12-01T08:19:46Z has_accepted_license: '1' intvolume: ' 135' issue: '21' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: Organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/trapping-particles-to-explain-lightning/ scopus_import: '1' status: public title: Using optical tweezers to simultaneously trap, charge, and measure the charge of a microparticle in air 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: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 135 year: '2025' ... --- _id: '20780' abstract: - lang: eng text: Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Lorena Alexandra full_name: Layana Franco, Lorena Alexandra id: 02814589-eb8f-11eb-b029-a70074f3f18f last_name: Layana Franco orcid: 0000-0002-1253-6297 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:10.15479/AT-ISTA-20780 apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20780 chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20780. ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria, 2025. ista: Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20780. mla: Layana Franco, Lorena Alexandra, et al. Causes and Consequences of Sex-Chromosome Turnovers in Diptera. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20780. short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025). corr_author: '1' date_created: 2025-12-10T23:40:14Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-06-10T08:27:48Z department: - _id: BeVi doi: 10.15479/AT-ISTA-20780 file: - access_level: open_access checksum: 251e7aab01917c2ad2fbccf465492ea1 content_type: application/zip creator: llayanaf date_created: 2025-12-11T10:47:15Z date_updated: 2025-12-11T10:47:15Z file_id: '20799' file_name: Perl_scripts.zip file_size: 4575 relation: main_file success: 1 - access_level: open_access checksum: daf1c03149dd170b14e5c8e109ee3c77 content_type: application/zip creator: llayanaf date_created: 2025-12-11T10:52:17Z date_updated: 2025-12-11T10:52:17Z file_id: '20800' file_name: Supplementary_Datasets.zip file_size: 19052849 relation: main_file success: 1 - access_level: open_access checksum: 658d6e95a361b0a3db058b7b4e1733d4 content_type: application/zip creator: llayanaf date_created: 2025-12-11T10:52:11Z date_updated: 2025-12-11T10:52:11Z file_id: '20801' file_name: Supplementary_Tables.zip file_size: 566476 relation: main_file success: 1 - access_level: open_access checksum: 2a2b92eb9fade0015719190596a8c5b7 content_type: text/plain creator: llayanaf date_created: 2025-12-11T11:00:53Z date_updated: 2025-12-11T11:00:53Z file_id: '20802' file_name: README.txt file_size: 1204 relation: main_file success: 1 file_date_updated: 2025-12-11T11:00:53Z has_accepted_license: '1' keyword: - Schizophora - sex chromosomes - sex-chromosome turnover - Diptera - genomic features - out-of-X movement. month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Causes and consequences of sex-chromosome turnovers in Diptera tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- OA_place: publisher OA_type: gold _id: '20819' abstract: - lang: eng text: "Clustering is a cornerstone of data analysis that is particularly suited to identifying coherent subgroups or substructures in unlabeled data, as are generated continuously in large amounts these days. However, in many cases traditional clustering methods are not applicable, because data are increasingly being produced and stored in a distributed way, e.g. on edge devices, and privacy concerns prevent it from being transferred to a central server. To address this challenge, we present FedDP-KMeans, a new algorithm for \r\n-means clustering that is fully-federated as well as differentially private. Our approach leverages (potentially small and out-of-distribution) server-side data to overcome the primary challenge of differentially private clustering methods: the need for a good initialization. Combining our initialization with a simple federated DP-Lloyds algorithm we obtain an algorithm that achieves excellent results on synthetic and real-world benchmark tasks. We also provide a theoretical analysis of our method that provides bounds on the convergence speed and cluster identification success." acknowledged_ssus: - _id: ScienComp acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF) [10.55776/COE12] and supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).\r\n" alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: David full_name: Saulpic, David id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964 last_name: Saulpic citation: ama: 'Scott JA, Lampert C, Saulpic D. Differentially private federated k-means clustering with server-side data. In: 42nd International Conference on Machine Learning. Vol 267. ML Research Press; 2025:53757-53790.' apa: 'Scott, J. A., Lampert, C., & Saulpic, D. (2025). Differentially private federated k-means clustering with server-side data. In 42nd International Conference on Machine Learning (Vol. 267, pp. 53757–53790). Vancouver, Canada: ML Research Press.' chicago: Scott, Jonathan A, Christoph Lampert, and David Saulpic. “Differentially Private Federated K-Means Clustering with Server-Side Data.” In 42nd International Conference on Machine Learning, 267:53757–90. ML Research Press, 2025. ieee: J. A. Scott, C. Lampert, and D. Saulpic, “Differentially private federated k-means clustering with server-side data,” in 42nd International Conference on Machine Learning, Vancouver, Canada, 2025, vol. 267, pp. 53757–53790. ista: 'Scott JA, Lampert C, Saulpic D. 2025. Differentially private federated k-means clustering with server-side data. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 53757–53790.' mla: Scott, Jonathan A., et al. “Differentially Private Federated K-Means Clustering with Server-Side Data.” 42nd International Conference on Machine Learning, vol. 267, ML Research Press, 2025, pp. 53757–90. short: J.A. Scott, C. Lampert, D. Saulpic, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 53757–53790. conference: end_date: 2025-07-19 location: Vancouver, Canada name: 'ICML: International Conference on Machine Learning' start_date: 2025-07-13 corr_author: '1' date_created: 2025-12-14T23:02:05Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-04-07T11:46:11Z day: '01' ddc: - '000' department: - _id: ChLa - _id: MoHe external_id: arxiv: - '2506.05408' file: - access_level: open_access checksum: 815b32b463023ca21e569c2158745c15 content_type: application/pdf creator: dernst date_created: 2025-12-16T12:38:29Z date_updated: 2025-12-16T12:38:29Z file_id: '20829' file_name: 2025_ICML_Scott.pdf file_size: 746612 relation: main_file success: 1 file_date_updated: 2025-12-16T12:38:29Z has_accepted_license: '1' intvolume: ' 267' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 53757-53790 publication: 42nd International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '21198' relation: dissertation_contains status: public scopus_import: '1' status: public title: Differentially private federated k-means clustering with server-side data 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 267 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '17468' abstract: - lang: eng text: Oxygen redox chemistry is central to life1 and many human-made technologies, such as in energy storage2,3,4. The large energy gain from oxygen redox reactions is often connected with the occurrence of harmful reactive oxygen species3,5,6. Key species are superoxide and the highly reactive singlet oxygen3,4,5,6,7, which may evolve from superoxide. However, the factors determining the formation of singlet oxygen, rather than the relatively unreactive triplet oxygen, are unknown. Here we report that the release of triplet or singlet oxygen is governed by individual Marcus normal and inverted region behaviour. We found that as the driving force for the reaction increases, the initially dominant evolution of triplet oxygen slows down, and singlet oxygen evolution becomes predominant with higher maximum kinetics. This behaviour also applies to the widely observed superoxide disproportionation, in which one superoxide is oxidized by another, in both non-aqueous and aqueous systems, with Lewis and Brønsted acidity controlling the driving forces. Singlet oxygen yields governed by these conditions are relevant, for example, in batteries or cellular organelles in which superoxide forms. Our findings suggest ways to understand and control spin states and kinetics in oxygen redox chemistry, with implications for fields, including life sciences, pure chemistry and energy storage. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: M-Shop - _id: ScienComp acknowledgement: S.A.F. thanks the Institute of Science and Technology Austria (ISTA) for the support. The Scientific Service Units of ISTA supported this research through resources provided by the Imaging and Optics Facility, the Lab Support Facility, the Miba Machine Shop and Scientific Computing. This research was partly funded by the Austrian Science Fund (FWF) (10.55776/P37169 and 10.55776/COE5). For open access purposes, the author has applied for a CC BY public copyright licence to any author-accepted manuscript version arising from this submission. R.H. acknowledges funding through CZI grant DAF2020-225401 (10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (10.13039/100014989). H.T.K.N. acknowledges funding by the European Commission Erasmus Mundus Joint Masters programme. We thank M. Sixt and M. Chinon for the discussions about O-redox in life and R. Jethwa for proofreading. Open access funding was provided by ISTA. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Huyen T.K. full_name: Nguyen, Huyen T.K. last_name: Nguyen - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. Nature. 2025;646(8085):601–605. doi:10.1038/s41586-025-09587-7 apa: Mondal, S., Nguyen, H. T. K., Hauschild, R., & Freunberger, S. A. (2025). Marcus kinetics control singlet and triplet oxygen evolving from superoxide. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-09587-7 chicago: Mondal, Soumyadip, Huyen T.K. Nguyen, Robert Hauschild, and Stefan Alexander Freunberger. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-09587-7. ieee: S. Mondal, H. T. K. Nguyen, R. Hauschild, and S. A. Freunberger, “Marcus kinetics control singlet and triplet oxygen evolving from superoxide,” Nature, vol. 646, no. 8085. Springer Nature, pp. 601–605, 2025. ista: Mondal S, Nguyen HTK, Hauschild R, Freunberger SA. 2025. Marcus kinetics control singlet and triplet oxygen evolving from superoxide. Nature. 646(8085), 601–605. mla: Mondal, Soumyadip, et al. “Marcus Kinetics Control Singlet and Triplet Oxygen Evolving from Superoxide.” Nature, vol. 646, no. 8085, Springer Nature, 2025, pp. 601–605, doi:10.1038/s41586-025-09587-7. short: S. Mondal, H.T.K. Nguyen, R. Hauschild, S.A. Freunberger, Nature 646 (2025) 601–605. corr_author: '1' date_created: 2024-08-29T10:40:23Z date_published: 2025-10-16T00:00:00Z date_updated: 2026-04-28T13:18:33Z day: '16' ddc: - '540' department: - _id: StFr - _id: Bio doi: 10.1038/s41586-025-09587-7 external_id: isi: - '001586378900001' pmid: - '41044415' file: - access_level: open_access checksum: b507ddd23df0388aa65d04dc9b00fe3d content_type: application/pdf creator: dernst date_created: 2025-10-20T10:26:13Z date_updated: 2025-10-20T10:26:13Z file_id: '20500' file_name: 2025_Nature_Mondal.pdf file_size: 3809247 relation: main_file success: 1 file_date_updated: 2025-10-20T10:26:13Z has_accepted_license: '1' intvolume: ' 646' isi: 1 issue: '8085' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 601–605 pmid: 1 project: - _id: 8df062be-16d5-11f0-9cad-f559b6612c7e grant_number: P37169 name: Singlet oxygen in non-aqueous oxygen redox chemistry - _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473 grant_number: CZI01 name: Tools for automation and feedback microscopy publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/taming-the-bad-oxygen/ scopus_import: '1' status: public title: Marcus kinetics control singlet and triplet oxygen evolving from superoxide 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: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 646 year: '2025' ... --- APC_amount: 12348 EUR OA_place: publisher OA_type: hybrid _id: '17884' abstract: - lang: eng text: Human T cell leukemia virus type 1 (HTLV-1) immature particles differ in morphology from other retroviruses, suggesting a distinct way of assembly. Here we report the results of cryo-electron tomography studies of HTLV-1 virus-like particles assembled in vitro, as well as derived from cells. This work shows that HTLV-1 uses a distinct mechanism of Gag–Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature capsid (CA) tubular arrays reveals that the primary stabilizing component in HTLV-1 is the N-terminal domain of CA. Mutagenesis analysis supports this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the C-terminal domain of CA. These results provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus and this helps explain why HTLV-1 particles are morphologically distinct. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: EM-Fac acknowledgement: This work was funded by the Institute of Science and Technology Austria (ISTA) and the Austrian Science Fund (grant P31445 to F.K.M.S.). Access to high-resolution cryo-ET data acquisition at European Molecular Biology Laboratory (EMBL) Heidelberg was supported through the EMBL cryo-EM platform. We thank V.-V. Hodirnau at ISTA and W. Hagen and F. Weis at EMBL Heidelberg for support in cryo-ET data acquisition. This research was also supported by the scientific service units of ISTA through resources provided by Scientific Computing, the Life Science Facility, and the EM Facility. L.M.M. was supported by National Institutes of Health grants R01 GM151775 and R21 DE032878 and by the University of Minnesota Masonic Cancer Center. D.P. was supported by the DOC doctoral fellowship program of the Austrian Academy of Sciences. R.A.D was supported by the National Institute of Allergy and Infectious Diseases (grant R01AI147890). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Specifically, we also want to thank A. Schlögl for computational support and J. Hansen and V. Vogt for critical comments on the manuscript. We also thank the other members of the Schur lab for helpful discussions and experimental advice. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Mathias full_name: Percipalle, Mathias id: 4986e21c-eb97-11eb-a6c2-a4ef0b629971 last_name: Percipalle - first_name: Darya full_name: Chernikova, Darya id: 7dbaf460-fa9e-11eb-b0ca-bc7c7ff21ad0 last_name: Chernikova - first_name: Huixin full_name: Yang, Huixin last_name: Yang - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Gergely full_name: Pinke, Gergely id: 4D5303E6-F248-11E8-B48F-1D18A9856A87 last_name: Pinke - first_name: Dario J full_name: Porley, Dario J id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87 last_name: Porley - first_name: Louis M. full_name: Mansky, Louis M. last_name: Mansky - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Obr M, Percipalle M, Chernikova D, et al. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural & Molecular Biology. 2025;32:268-276. doi:10.1038/s41594-024-01390-8 apa: Obr, M., Percipalle, M., Chernikova, D., Yang, H., Thader, A., Pinke, G., … Schur, F. K. (2025). Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01390-8 chicago: Obr, Martin, Mathias Percipalle, Darya Chernikova, Huixin Yang, Andreas Thader, Gergely Pinke, Darío Porley Esteves, Louis M. Mansky, Robert A. Dick, and Florian KM Schur. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01390-8. ieee: M. Obr et al., “Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice,” Nature Structural & Molecular Biology, vol. 32. Springer Nature, pp. 268–276, 2025. ista: Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley Esteves D, Mansky LM, Dick RA, Schur FK. 2025. Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice. Nature Structural & Molecular Biology. 32, 268–276. mla: Obr, Martin, et al. “Distinct Stabilization of the Human T Cell Leukemia Virus Type 1 Immature Gag Lattice.” Nature Structural & Molecular Biology, vol. 32, Springer Nature, 2025, pp. 268–76, doi:10.1038/s41594-024-01390-8. short: M. Obr, M. Percipalle, D. Chernikova, H. Yang, A. Thader, G. Pinke, D. Porley Esteves, L.M. Mansky, R.A. Dick, F.K. Schur, Nature Structural & Molecular Biology 32 (2025) 268–276. corr_author: '1' date_created: 2024-09-08T10:29:06Z date_published: 2025-02-01T00:00:00Z date_updated: 2026-03-16T12:55:18Z day: '01' ddc: - '570' department: - _id: FlSc - _id: LeSa doi: 10.1038/s41594-024-01390-8 external_id: isi: - '001306564000001' oaworkid: - W4402316284 pmid: - '39242978' file: - access_level: open_access checksum: c641ad94afb28917b20425db676fc3ee content_type: application/pdf creator: dernst date_created: 2025-04-23T07:02:33Z date_updated: 2025-04-23T07:02:33Z file_id: '19608' file_name: 2025_NatureStrucBio_Obr.pdf file_size: 13724041 relation: main_file success: 1 file_date_updated: 2025-04-23T07:02:33Z has_accepted_license: '1' intvolume: ' 32' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version oaworkid: 1 page: 268-276 pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid - _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A grant_number: '25762' name: Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Distinct stabilization of the human T cell leukemia virus type 1 immature Gag lattice 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: repository OA_type: green _id: '20804' abstract: - lang: eng text: RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters the nucleus, where it transcribes protein-coding genes. Although transcription by Pol II is intensively studied, how this central multi-subunit enzyme is made and the role of dedicated factors remains unclear. Here, we report the integrative structural analysis of a native human Pol II from the cytoplasm captured near the end of biogenesis. The complex contained Gdown1 and three biogenesis factors – RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the complex revealed how Gdown1 and RPAP2 associate with Pol II and prevent the premature association of transcription factors. Further biochemical and cryo-EM analysis revealed how RPAP2 recruits GPN1–GPN3 to the complex, and how the assembly of the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results uncover a network of interactions that chaperone cytoplasmic Pol II to prevent aberrant interactions, reveal a GTP-controlled switch during the final stages of Pol II biogenesis, and suggest a general mechanism for the action of GPN-loop GTPase family of enzymes. acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp - _id: PreCl acknowledgement: We thank A. Salmazo for assistance with Pol II purification. We thank staff at the VBCF Proteomics facility for immunoprecipitation-mass spectrometry analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research was further supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF). article_processing_charge: No author: - first_name: Annamaria full_name: Hlavata, Annamaria id: 36062FEC-F248-11E8-B48F-1D18A9856A87 last_name: Hlavata - first_name: Benjamin full_name: Neuditschko, Benjamin last_name: Neuditschko - first_name: Ulla full_name: Schellhaas, Ulla last_name: Schellhaas - first_name: Clemens full_name: Plaschka, Clemens last_name: Plaschka - first_name: Franz full_name: Herzog, Franz last_name: Herzog - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 biorxivid: 1 citation: ama: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. bioRxiv. 2025. doi:10.64898/2025.12.10.692585 apa: Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., & Bernecky, C. (2025). Structure of cytoplasmic RNA polymerase II. bioRxiv. https://doi.org/10.64898/2025.12.10.692585 chicago: Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka, Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.” BioRxiv, 2025. https://doi.org/10.64898/2025.12.10.692585. ieee: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C. Bernecky, “Structure of cytoplasmic RNA polymerase II,” bioRxiv. 2025. ista: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. 2025. Structure of cytoplasmic RNA polymerase II. bioRxiv, 10.64898/2025.12.10.692585. mla: Hlavata, Annamaria, et al. “Structure of Cytoplasmic RNA Polymerase II.” BioRxiv, 2025, doi:10.64898/2025.12.10.692585. short: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky, BioRxiv (2025). corr_author: '1' date_created: 2025-12-11T13:33:27Z date_published: 2025-12-10T00:00:00Z date_updated: 2026-07-22T06:51:50Z day: '10' ddc: - '570' department: - _id: CaBe doi: 10.64898/2025.12.10.692585 external_id: biorxivid: - 10.64898/2025.12.10.692585 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.64898/2025.12.10.692585 month: '12' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: published status: public title: Structure of cytoplasmic RNA polymerase II 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: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '19431' abstract: - lang: eng text: "Gene expression is crucial for cell differentiation, development and survival of\r\norganisms. It consists of several steps, starting with transcription that is mediated by\r\nRNA polymerases. These are protein machineries transcribing and producing different\r\ntypes of RNAs. Although, the individual steps of transcription by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively studied, surprisingly,\r\nthere is still little known about its regulation and assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in this process. Techniques of structural\r\nbiology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners.\r\nThis study shows for the first time the structure of cytoplasmic Pol II at high\r\nresolution. The structure also reveals proteins interacting with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric clashes with various transcription\r\nfactors bound to Pol II during different stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins on Pol II and several experiments suggest that they interact with the\r\nclamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially open state. Based on these results I propose a novel model of regulation of\r\nPol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis research contributes to the current knowledge of molecular mechanisms\r\nof Pol II regulation in cytoplasm." acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp acknowledgement: 'I would also like to acknowledge the ISTA Facilities: Lab Support Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific Computing. EMF for their support during data collections and troubleshooting, especially Valentin. Scientific Computing for solving quickly any issues related with cluster.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Annamaria full_name: Hlavata, Annamaria id: 36062FEC-F248-11E8-B48F-1D18A9856A87 last_name: Hlavata citation: ama: Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:10.15479/10.15479/AT-ISTA-19431 apa: Hlavata, A. (2025). Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria. https://doi.org/10.15479/10.15479/AT-ISTA-19431 chicago: Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/AT-ISTA-19431. ieee: A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science and Technology Austria, 2025. ista: Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria. mla: Hlavata, Annamaria. Regulation of Cytoplasmic RNA Polymerase II. Institute of Science and Technology Austria, 2025, doi:10.15479/10.15479/AT-ISTA-19431. short: A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-20T12:52:47Z date_published: 2025-03-20T00:00:00Z date_updated: 2026-04-07T11:46:32Z day: '20' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: CaBe doi: 10.15479/10.15479/AT-ISTA-19431 file: - access_level: closed checksum: b7ddf424ffe95f8c767c53c8bb62d4f3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ahlavata date_created: 2025-03-24T12:48:36Z date_updated: 2026-03-20T23:30:04Z embargo_to: open_access file_id: '19448' file_name: PhD_Thesis_Hlavata_final_submission.docx file_size: 23506747 relation: source_file - access_level: open_access checksum: 6c5a59c9bac467c3d0b3ffb8ea6d9fd4 content_type: application/pdf creator: ahlavata date_created: 2025-03-24T12:51:10Z date_updated: 2026-03-20T23:30:04Z embargo: 2026-03-20 file_id: '19449' file_name: PhD_Thesis_Hlavata_final_submission_update.pdf file_size: 9478591 relation: main_file file_date_updated: 2026-03-20T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '83' publication_identifier: eissn: - 2663-337X isbn: - 978-3-99078-055-8 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 title: Regulation of Cytoplasmic RNA Polymerase II type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19533' abstract: - lang: eng text: "This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n" acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: SSU acknowledgement: "I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 citation: ama: Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:10.15479/AT-ISTA-19533 apa: Sett, R. (2025). Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19533 chicago: Sett, Riya. “ Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19533. ieee: R. Sett, “ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025. ista: Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. mla: Sett, Riya. Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19533. short: R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-09T16:44:26Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-06-03T07:16:05Z day: '1' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-19533 ec_funded: 1 file: - access_level: open_access checksum: ba6cd2289d0141a160a14fc97df1632f content_type: application/pdf creator: rsett date_created: 2025-04-10T11:33:22Z date_updated: 2025-10-11T22:30:02Z embargo: 2025-10-11 file_id: '19538' file_name: PhD_Thesis_Riya_Sett_pdfa.pdf file_size: 4129208 relation: main_file - access_level: closed checksum: ee63a94cb8f7adf5e766903028b81ed6 content_type: application/x-zip-compressed creator: rsett date_created: 2025-04-10T11:34:08Z date_updated: 2025-10-11T22:30:02Z embargo_to: open_access file_id: '19539' file_name: PhD Thesis Riya Sett.zip file_size: 6646110 relation: source_file file_date_updated: 2025-10-11T22:30:02Z has_accepted_license: '1' keyword: - phase transition - open quantum system - phase diagram - cavity quantum electrodynamics - superconducting qubits - semiclassical physics - quantum optics - josephson junction - parametric converter - phase conjugation - quantum radar - quantum entanglement - correlation - quantum sensing language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '109' project: - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _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: '18978' relation: research_data status: public - id: '19280' relation: part_of_dissertation status: public - id: '17183' relation: part_of_dissertation status: public - id: '13117' 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: ' Quantum remote sensing and non-equilibrium phase transitions in the microwave regime' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19735' abstract: - lang: eng text: The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome. acknowledged_ssus: - _id: ScienComp acknowledgement: We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA. article_number: msaf085 article_processing_charge: Yes article_type: original author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Minerva S full_name: Trejo Arellano, Minerva S id: 2b681148-eed5-11eb-b81b-ae229e8620f8 last_name: Trejo Arellano orcid: 0000-0002-1982-3475 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 2025;42(5). doi:10.1093/molbev/msaf085 apa: Bett, V. K., Trejo Arellano, M. S., & Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msaf085 chicago: Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” Molecular Biology and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf085. ieee: V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” Molecular Biology and Evolution, vol. 42, no. 5. Oxford University Press, 2025. ista: Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085. mla: Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” Molecular Biology and Evolution, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:10.1093/molbev/msaf085. short: V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025). corr_author: '1' date_created: 2025-05-25T22:16:56Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-07-26T22:30:33Z day: '01' ddc: - '570' department: - _id: BeVi - _id: DaZi doi: 10.1093/molbev/msaf085 external_id: isi: - '001483460200001' pmid: - '40202086' file: - access_level: open_access checksum: 6c14b03f94b4aadf8869be2c4366d077 content_type: application/pdf creator: dernst date_created: 2025-05-28T09:34:36Z date_updated: 2025-05-28T09:34:36Z file_id: '19756' file_name: 2025_MBE_Bett.pdf file_size: 1282772 relation: main_file success: 1 file_date_updated: 2025-05-28T09:34:36Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git record: - id: '20449' relation: dissertation_contains status: public - id: '20444' relation: dissertation_contains status: deleted scopus_import: '1' status: public title: Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana 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: 42 year: '2025' ... --- OA_place: publisher _id: '20449' abstract: - lang: eng text: "Males and females of many species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. " acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett citation: ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449 apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449 chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449. ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025. ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449. short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-11T08:18:51Z date_published: 2025-10-10T00:00:00Z date_updated: 2026-06-12T08:32:16Z day: '10' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-20449 file: - access_level: open_access checksum: 26905c22bca417198a733d792d8ce422 content_type: application/pdf creator: vbett date_created: 2025-10-20T13:32:29Z date_updated: 2026-06-01T22:30:04Z embargo: 2026-06-01 file_id: '20507' file_name: 2025_Bett_Vincent_Thesis.pdf file_size: 18507283 relation: main_file - access_level: closed checksum: 6a09a8d126d3628bfd8a35202735f267 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vbett date_created: 2025-10-20T13:35:34Z date_updated: 2026-06-01T22:30:04Z embargo_to: open_access file_id: '20508' file_name: 2025_Bett_Vincent_Thesis.docx file_size: 17163921 relation: source_file file_date_updated: 2026-06-01T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '114' project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19735' relation: part_of_dissertation status: public - id: '15009' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Evolution and regulation of the Z chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20694' abstract: - lang: eng text: "Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 citation: ama: Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:10.15479/AT-ISTA-20694 apa: Pal, A. (2025). Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694 chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694. ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025. ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694. short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-11-25T13:19:11Z date_published: 2025-11-25T00:00:00Z date_updated: 2026-04-28T13:20:36Z day: '25' ddc: - '576' - '578' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20694 file: - access_level: open_access checksum: 7a10a738d58524aebb5dcbd9b34c21c5 content_type: application/pdf creator: apal date_created: 2025-12-01T13:53:36Z date_updated: 2026-03-01T23:30:03Z embargo: 2026-03-01 file_id: '20721' file_name: 2025_Pal_Arka_Thesis.pdf file_size: 42723135 relation: main_file - access_level: closed checksum: 166d832b08d0434ce407f8f3cb930fe5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: apal date_created: 2025-12-01T13:53:39Z date_updated: 2026-03-01T23:30:03Z embargo_to: open_access file_id: '20722' file_name: 2025_Pal_Arka_Thesis.docx file_size: 60632116 relation: source_file file_date_updated: 2026-03-01T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '268' project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12159' relation: part_of_dissertation status: public - id: '14796' relation: part_of_dissertation status: public - id: '20190' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Using genealogies to study the genomic basis of species divergence 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20190' abstract: - lang: eng text: 'A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.' acknowledged_ssus: - _id: ScienComp acknowledgement: 'We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other Barton Group and Coop Lab members for stimulating discussions. We are grateful to all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón Mateu for her assistance in fieldwork logistics at the field station, El Serrat. We are grateful to Enrico Coen and his research group for providing the Antirrhinum molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up with sampling led by D.L.F. in 2017. The study was supported by Austrian Science Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.). Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics and analyses was provided by ISTA High Performance Cluster. ' article_number: e70067 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Alan full_name: Le Moan, Alan last_name: Le Moan - first_name: Adrian J. full_name: Mcnairn, Adrian J. last_name: Mcnairn - first_name: Jennifer K. full_name: Grenier, Jennifer K. last_name: Grenier - first_name: Marek full_name: Kucka, Marek last_name: Kucka - first_name: Graham full_name: Coop, Graham last_name: Coop - first_name: Yingguang Frank full_name: Chan, Yingguang Frank last_name: Chan - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 2025;34(22). doi:10.1111/mec.70067 apa: Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka, M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70067 chicago: Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K. Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70067. ieee: A. Pal et al., “Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum,” Molecular Ecology, vol. 34, no. 22. Wiley, 2025. ista: Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067. mla: Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology, vol. 34, no. 22, e70067, Wiley, 2025, doi:10.1111/mec.70067. short: A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G. Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025). corr_author: '1' date_created: 2025-08-17T22:01:37Z date_published: 2025-11-01T00:00:00Z date_updated: 2026-07-26T22:30:33Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/mec.70067 external_id: isi: - '001546622100001' file: - access_level: open_access checksum: c586fc674df4e7dd6e43aef87a52c6f6 content_type: application/pdf creator: dernst date_created: 2026-01-05T13:47:47Z date_updated: 2026-01-05T13:47:47Z file_id: '20958' file_name: 2025_MolecEcology_Pal.pdf file_size: 9886694 relation: main_file success: 1 file_date_updated: 2026-01-05T13:47:47Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Molecular Ecology publication_identifier: eissn: - 1365-294X issn: - 0962-1083 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/snapdragon-secrets/ record: - id: '20694' relation: dissertation_contains status: public scopus_import: '1' status: public title: Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum 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: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 34 year: '2025' ...