--- OA_place: publisher _id: '21957' abstract: - lang: eng text: "This thesis investigates algorithmic certification and approximation methods for degenerate semidefinite programs (SDPs) and the singular roots of polynomial systems. In the first part, we present a hybrid symbolic-numeric algorithm for certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating linear matrix inequalities (LMIs) into a structured polynomial system via facial reduction and incidence varieties, we guarantee the existence of an isolated exact solution. This algebraic reduction enables the certification of maximum-rank numerical approximations using methods from algebraic geometry.\r\n\r\nIn the second part, we address the severe ill-conditioning and loss of quadratic convergence that plague standard path-tracking methods near isolated singular roots. To overcome this, we propose tracking algorithms that achieve superlinear convergence without the computational bloat characteristic of classical deflation techniques. By modeling the solution path as a generalized fractional Puiseux series, our approach combines an explicitly derived algebraic predictor with a localized hyperplane desingularization phase during the corrector step. Furthermore, we introduce a continuous path-limit method and an extension of the geometric sequence rule to directly extract exact fractional exponents. This bypasses traditional heuristic trial-and-error methods and explicitly accommodates sparse series expansions. Numerical experiments confirm that our method significantly reduces the cumulative number of matrix inversions while achieving high-accuracy root approximations, even for heavily degenerate systems exhibiting higher coranks." acknowledgement: 'Funding: Vienna Graduate School on Computational Optimization (FWF), grant DOI: 10.55776/W1260.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jeferson full_name: Zapata, Jeferson id: 00223538-AF8F-11E9-A4C7-F729E6697425 last_name: Zapata citation: ama: 'Zapata J. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. 2026. doi:10.15479/AT-ISTA-21957' apa: 'Zapata, J. (2026). Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21957' chicago: 'Zapata, Jeferson. “Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21957.' ieee: 'J. Zapata, “Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames,” Institute of Science and Technology Austria, 2026.' ista: 'Zapata J. 2026. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria.' mla: 'Zapata, Jeferson. Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21957.' short: 'J. Zapata, Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '1' date_created: 2026-06-08T13:29:52Z date_published: 2026-06-09T00:00:00Z date_updated: 2026-07-27T14:30:42Z day: '09' ddc: - '500' degree_awarded: PhD department: - _id: GradSch - _id: VlKo doi: 10.15479/AT-ISTA-21957 doi_confirm: '1' file: - access_level: closed checksum: b11a959e99d3dcf61040282b5c837141 content_type: application/zip creator: jzapata date_created: 2026-06-08T13:20:02Z date_updated: 2026-06-08T13:20:02Z file_id: '21958' file_name: istaustriathesis_JZapata.zip file_size: 40811933 relation: source_file - access_level: open_access checksum: edf1e5899b2e31505cd1aa3fe8bd4b7f content_type: application/pdf creator: jzapata date_created: 2026-06-10T13:33:25Z date_updated: 2026-06-10T13:33:25Z file_id: '21992' file_name: 4_Final_Thesis_JZapata_REX.pdf file_size: 2207892 relation: main_file success: 1 file_date_updated: 2026-06-10T13:33:25Z fulldoi: https://doi.org/10.15479/AT-ISTA-21957 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '06' oa: 1 oa_version: Published Version page: '89' project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: isbn: - 978-3-99078-079-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21144' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov title: 'Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames' 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: '2026' ... --- OA_place: repository _id: '21360' acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "I would like to acknowledge the Austrian Academy of Sciences (ÖAW) and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 citation: ama: 'Riegler S. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:10.15479/AT-ISTA-21360' apa: 'Riegler, S. (2026). Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21360' chicago: 'Riegler, Stefan. “Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21360.' ieee: 'S. Riegler, “Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species,” Institute of Science and Technology Austria, 2026.' ista: 'Riegler S. 2026. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria.' mla: 'Riegler, Stefan. Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21360.' short: 'S. Riegler, Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '1' date_created: 2026-02-27T09:08:14Z date_published: 2026-02-26T00:00:00Z date_updated: 2026-07-27T14:30:08Z day: '26' ddc: - '570' - '575' - '583' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-21360 doi_confirm: '1' file: - access_level: closed checksum: 2f1f44e8536c2538f94a440217452c9f content_type: application/x-zip-compressed creator: sriegler date_created: 2026-03-02T10:59:50Z date_updated: 2026-03-02T10:59:50Z file_id: '21386' file_name: 2026_Riegler_Stefan_Thesis.zip file_size: 31430022 relation: source_file - access_level: closed checksum: 2e8dc39640bc26ae5684c944c619719b content_type: application/pdf creator: sriegler date_created: 2026-03-02T10:59:49Z date_updated: 2026-03-02T10:59:49Z embargo: 2027-02-27 embargo_to: open_access file_id: '21387' file_name: 2026_Riegler_Stefan_Thesis.pdf file_size: 11635090 relation: main_file file_date_updated: 2026-03-02T10:59:50Z fulldoi: https://doi.org/10.15479/AT-ISTA-21360 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '02' oa_version: Published Version page: '185' project: - _id: 34afa094-11ca-11ed-8bc3-a375845a59fb grant_number: '101060393' name: Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21363' relation: research_data status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: 'Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- _id: '21363' abstract: - lang: eng text: The data contains information on coffee differential gene expression as well as co-expression and trait correlations in two separate experiments. First, contrasting nitrogen supply, second, intra- and interspecific grafting. article_processing_charge: No author: - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 citation: ama: 'Riegler S. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:10.15479/AT-ISTA-21363' apa: 'Riegler, S. (2026). Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21363' chicago: 'Riegler, Stefan. “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21363.' ieee: 'S. Riegler, “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species.” Institute of Science and Technology Austria, 2026.' ista: 'Riegler S. 2026. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21363.' mla: 'Riegler, Stefan. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21363.' short: S. Riegler, (2026). contributor: - contributor_type: supervisor first_name: Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 corr_author: '1' date_created: 2026-02-27T09:18:41Z date_published: 2026-02-27T00:00:00Z date_updated: 2026-07-27T14:30:07Z day: '27' ddc: - '575' department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-21363 file: - access_level: closed checksum: de9145fa166a28c588b5184a2d3d4fee content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: sriegler date_created: 2026-02-27T09:11:33Z date_updated: 2026-02-27T09:11:33Z embargo: 2027-02-27 embargo_to: open_access file_id: '21364' file_name: SupplementaryTables.xlsx file_size: 63749444 relation: main_file - access_level: closed checksum: ce1f163551c96cee45943a8ea29720b6 content_type: text/plain creator: sriegler date_created: 2026-02-27T09:13:11Z date_updated: 2026-02-27T09:13:11Z embargo: 2027-02-27 embargo_to: open_access file_id: '21365' file_name: ReadMe.txt file_size: 124 relation: main_file file_date_updated: 2026-02-27T09:13:11Z fulldoi: https://doi.org/10.15479/AT-ISTA-21363 has_accepted_license: '1' month: '02' oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '21360' relation: used_in_publication status: public status: public title: 'Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21980' abstract: - lang: eng text: Despite significant progress in the field of molecular electronics over the last two decades, the quantitative prediction of metal-molecule-metal junction conductance remains a challenge. The standard computational framework combines density functional theory (DFT) with nonequilibrium Green’s functions (NEGF) using low-rung exchange-correlation functionals such as PBE, which overestimate the conductances. More advanced correction methods exist but require complex workflows and high computational cost, limiting their accessibility. Here, we introduce a physically motivated approach that approximates results obtained with high-rung functionals. Our method fits the PBE-calculated transmission to a Breit-Wigner form and subsequently refines the fit parameters using molecular orbital energies and metal densities of states computed for the isolated subsystems with high-rung functionals. This approach is applicable to a broad range of molecular junctions yielding conductance values in quantitative agreement with experiments. Our approach is simple, low-cost, and accurate, making it well-suited for routine and large-scale prediction of single-molecule junction conductance. acknowledgement: This work was supported primarily by the Institute of Science and Technology Austria. L.V. was supported in part by the National Science Foundation (No. NSF-DMR 2241180). Z.-F.L. was supported by an NSF CAREER Award, No. DMR-2044552 and an Alfred P. Sloan Research Fellowship, No. FG-2024-21750. article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Artem full_name: Gulyaev, Artem id: 83ed7901-7380-11f0-bf20-a0788d5e654d last_name: Gulyaev - first_name: Jyotisman full_name: Hazarika, Jyotisman id: d87714c4-663d-11f0-bd06-caece19833e5 last_name: Hazarika orcid: 0009-0007-2542-7878 - first_name: Zhen-Fei full_name: Liu, Zhen-Fei last_name: Liu - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 chemrxivid: 1 citation: ama: Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 2026;26(22):7429–7434. doi:10.1021/acs.nanolett.6c01462 apa: Gulyaev, A., Hazarika, J., Liu, Z.-F., & Venkataraman, L. (2026). A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.6c01462 chicago: Gulyaev, Artem, Jyotisman Hazarika, Zhen-Fei Liu, and Latha Venkataraman. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” Nano Letters. American Chemical Society, 2026. https://doi.org/10.1021/acs.nanolett.6c01462. ieee: A. Gulyaev, J. Hazarika, Z.-F. Liu, and L. Venkataraman, “A computationally efficient and accurate method for predicting conductance of single-molecule junctions,” Nano Letters, vol. 26, no. 22. American Chemical Society, pp. 7429–7434, 2026. ista: Gulyaev A, Hazarika J, Liu Z-F, Venkataraman L. 2026. A computationally efficient and accurate method for predicting conductance of single-molecule junctions. Nano Letters. 26(22), 7429–7434. mla: Gulyaev, Artem, et al. “A Computationally Efficient and Accurate Method for Predicting Conductance of Single-Molecule Junctions.” Nano Letters, vol. 26, no. 22, American Chemical Society, 2026, pp. 7429–7434, doi:10.1021/acs.nanolett.6c01462. short: A. Gulyaev, J. Hazarika, Z.-F. Liu, L. Venkataraman, Nano Letters 26 (2026) 7429–7434. corr_author: '1' das_tickbox: '1' date_created: 2026-06-10T07:27:19Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-28T09:57:28Z day: '01' ddc: - '540' department: - _id: LaVe - _id: GradSch doi: 10.1021/acs.nanolett.6c01462 external_id: chemrxivid: - 10.26434/chemrxiv.15001696 pmid: - '42223342' file: - access_level: open_access checksum: 897551374cac28e0db26dcb0b676b8e7 content_type: application/pdf creator: dernst date_created: 2026-06-16T09:11:35Z date_updated: 2026-06-16T09:11:35Z file_id: '22013' file_name: 2026_NanoLetters_Gulyaev.pdf file_size: 3362800 relation: main_file success: 1 file_date_updated: 2026-06-16T09:11:35Z fulldoi: https://doi.org/10.1021/acs.nanolett.6c01462 has_accepted_license: '1' intvolume: ' 26' issue: '22' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 7429–7434 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: A computationally efficient and accurate method for predicting conductance of single-molecule junctions 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: 26 year: '2026' ... --- OA_place: repository OA_type: green _id: '22404' abstract: - lang: eng text: We consider a class of two-dimensional tight binding models displaying conical intersections of the Bloch bands at the Fermi level. The setting includes the case of generic transitions between quantum Hall phases. We consider the longitudinal conductivity, as given by Kubo formula, describing the variation of the current after introducing a space-homogeneous electric field, in an adiabatic way. We obtain an explicit expression for the longitudinal conductivity, completely determined by the number of conical intersections and by the shape of the cones. In particular, the formula reproduces the known quantized values found for graphene and for the critical Haldane model. Furthermore, we discuss the validity of Kubo formula in presence of conical intersections in the spectrum, starting from the time-dependent Schrödinger equation. For electric fields which are weak and slowly varying in space and in time, we prove the validity of linear response from quantum dynamics. acknowledgement: G. M. and M. P. acknowledge support by the European Research Council through the ERC-StG MaMBoQ, n. 802901. G. M. acknowledges financial support from the Independent Research Fund Denmark–Natural Sciences, grant DFF–10.46540/2032-00005B and from the European Research Council through the ERC CoG UniCoSM, grant agreement n.724939. M. P. acknowledges support from the MUR, PRIN 2022 project MaIQuFi cod. 20223J85K3. This work has been carried out under the auspices of the GNFM of INdAM. We thank the anonymous referees for comments on a previous version of this manuscript. article_number: '82' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Giovanna full_name: Marcelli, Giovanna last_name: Marcelli - first_name: Lorenzo full_name: Pigozzi, Lorenzo id: efb8f850-3208-11ee-ac71-8c4f5803b9c6 last_name: Pigozzi - first_name: Marcello full_name: Porta, Marcello last_name: Porta citation: ama: Marcelli G, Pigozzi L, Porta M. Longitudinal conductivity at integer quantum Hall transitions. Letters in Mathematical Physics. 2026;116(4). doi:10.1007/s11005-026-02087-3 apa: Marcelli, G., Pigozzi, L., & Porta, M. (2026). Longitudinal conductivity at integer quantum Hall transitions. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-026-02087-3 chicago: Marcelli, Giovanna, Lorenzo Pigozzi, and Marcello Porta. “Longitudinal Conductivity at Integer Quantum Hall Transitions.” Letters in Mathematical Physics. Springer Nature, 2026. https://doi.org/10.1007/s11005-026-02087-3. ieee: G. Marcelli, L. Pigozzi, and M. Porta, “Longitudinal conductivity at integer quantum Hall transitions,” Letters in Mathematical Physics, vol. 116, no. 4. Springer Nature, 2026. ista: Marcelli G, Pigozzi L, Porta M. 2026. Longitudinal conductivity at integer quantum Hall transitions. Letters in Mathematical Physics. 116(4), 82. mla: Marcelli, Giovanna, et al. “Longitudinal Conductivity at Integer Quantum Hall Transitions.” Letters in Mathematical Physics, vol. 116, no. 4, 82, Springer Nature, 2026, doi:10.1007/s11005-026-02087-3. short: G. Marcelli, L. Pigozzi, M. Porta, Letters in Mathematical Physics 116 (2026). das_tickbox: '1' dataavailabilitystatement: Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study. date_created: 2026-07-26T22:01:40Z date_published: 2026-08-01T00:00:00Z date_updated: 2026-07-29T10:51:55Z day: '01' department: - _id: RoSe - _id: GradSch doi: 10.1007/s11005-026-02087-3 external_id: arxiv: - '2503.01381' fulldoi: https://doi.org/10.1007/s11005-026-02087-3 intvolume: ' 116' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2503.01381 mathsc: - 81V70 month: '08' oa: 1 oa_version: Preprint publication: Letters in Mathematical Physics publication_identifier: eissn: - 1573-0530 issn: - 0377-9017 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: no title: Longitudinal conductivity at integer quantum Hall transitions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 116 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22607' abstract: - lang: eng text: "Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\".\r\nCode: https://github.com/madvorak/duality/tree/v3.2.0" acknowledgement: "We would like to thank David Bartl and Jasmin Blanchette for frequent consultations.\r\nWe would also like to express gratitude to Henrik Böving for a help with generalization\r\nfrom extended rationals to extended linearly ordered fields and to Andrew Yang for the\r\nproof of Finset.univ_sum_of_zero_when_not. We would also like to acknowledge Antoine\r\nChambert-Loir, Apurva Nakade, Yaël Dillies, Richard Copley, Edward van de Meent, Markus\r\nHimmel, Mario Carneiro, and Kevin Buzzard." article_number: '14253' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2026;2. doi:10.46298/afm.14253 apa: Dvorak, M., & Kolmogorov, V. (2026). Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. EPI Sciences. https://doi.org/10.46298/afm.14253 chicago: Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” Annals of Formalized Mathematics. EPI Sciences, 2026. https://doi.org/10.46298/afm.14253. ieee: M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” Annals of Formalized Mathematics, vol. 2. EPI Sciences, 2026. ista: Dvorak M, Kolmogorov V. 2026. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2, 14253. mla: Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” Annals of Formalized Mathematics, vol. 2, 14253, EPI Sciences, 2026, doi:10.46298/afm.14253. short: M. Dvorak, V. Kolmogorov, Annals of Formalized Mathematics 2 (2026). corr_author: '1' das_tickbox: '0' date_created: 2026-07-29T09:06:55Z date_published: 2026-03-13T00:00:00Z date_updated: 2026-07-29T10:50:17Z day: '13' ddc: - '500' department: - _id: VlKo - _id: GradSch doi: 10.46298/afm.14253 external_id: arxiv: - '2409.08119' fulldoi: https://doi.org/10.46298/afm.14253 has_accepted_license: '1' intvolume: ' 2' keyword: - Farkas lemma - linear programming - extended reals - calculus of inductive constructions language: - iso: eng mathsc: - 68V20 - 15A39 - 90C05 month: '03' oa_version: Published Version publication: Annals of Formalized Mathematics publication_identifier: eissn: - 3117-4604 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '20071' relation: earlier_version status: public researchdata_availability: no status: public supplementarymaterial: no title: Duality theory in linear optimization and its extensions -- formally verified 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: 2 year: '2026' ... --- OA_place: repository _id: '21393' abstract: - lang: eng text: "This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X citation: ama: 'Dvorak M. Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids. 2026. doi:10.15479/AT-ISTA-21393' apa: 'Dvorak, M. (2026). Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21393' chicago: 'Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4: Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21393.' ieee: 'M. Dvorak, “Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026.' ista: 'Dvorak M. 2026. Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria.' mla: 'Dvorak, Martin. Pursuit of Truth and Beauty in Lean 4: Formally Verified Theory of Grammars, Optimization, Matroids. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21393.' short: 'M. Dvorak, Pursuit of Truth and Beauty in Lean 4: Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-03-04T09:26:46Z date_published: 2026-03-04T00:00:00Z date_updated: 2026-07-29T12:56:52Z day: '04' ddc: - '511' - '000' degree_awarded: PhD department: - _id: GradSch - _id: VlKo doi: 10.15479/AT-ISTA-21393 doi_confirm: '1' file: - access_level: open_access checksum: cface6dc18152680962b5361575f6e4f content_type: application/pdf creator: mdvorak date_created: 2026-03-04T08:56:15Z date_updated: 2026-03-04T08:56:15Z file_id: '21394' file_name: 2026_Dvorak_Martin_Thesis.pdf file_size: 1771231 relation: main_file success: 1 - access_level: closed checksum: 290ddfacfb7e07fb07e6f0b334e67c90 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mdvorak date_created: 2026-03-04T09:03:37Z date_updated: 2026-03-04T09:03:37Z file_id: '21395' file_name: 2026_Dvorak_Martin_Thesis.docx file_size: 864585 relation: source_file file_date_updated: 2026-03-04T09:03:37Z fulldoi: https://doi.org/10.15479/AT-ISTA-21393 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '160' publication_identifier: isbn: - 978-3-99078-074-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: link: - description: Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality) relation: software url: https://github.com/madvorak/duality/tree/v3.5.0 - description: Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems) relation: software url: https://github.com/madvorak/vcsp/tree/v8.2.0 - description: Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project) relation: software url: https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0 - description: Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars) relation: software url: https://github.com/madvorak/chomsky/tree/v1.2.0 - description: Old version (Lean 3) of the project about grammars relation: software url: https://github.com/madvorak/grammars - description: Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis relation: software url: https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean record: - id: '13120' relation: part_of_dissertation status: public - id: '20071' relation: part_of_dissertation status: public - id: '21398' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Jasmin full_name: Blanchette, Jasmin last_name: Blanchette title: 'Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids' 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: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22406' abstract: - lang: eng text: "It is known that for a uniform morphic sequence \U0001D496 =⟨\U0001D462\U0001D45B⟩∞\r\n\U0001D45B=0 and an algebraic number \U0001D6FD such that |\U0001D6FD| >1, the number [[\U0001D496]]\U0001D6FD :=∑∞\r\n\U0001D45B=0(\U0001D462\U0001D45B/\U0001D6FD\U0001D45B) either lies in ℚ⁡(\U0001D6FD) or is transcendental. In this paper, we show a similar rational–transcendental dichotomy for sequences defined by irreducible Pisot morphisms on binary alphabets. Subject to the Pisot conjecture (an irreducible Pisot morphism has pure discrete spectrum), we generalise the latter result to arbitrary finite alphabets. In certain cases, we are able to show transcendence of [[\U0001D496]]\U0001D6FD outright. In particular, for \U0001D458 ≥2, if \U0001D496 is the k-Bonacci word, then [[\U0001D496]]\U0001D6FD is transcendental." acknowledgement: "We thank the anonymous referee for identifying an error in an earlier\r\nversion of the paper. We gratefully acknowledge support from UKRI Frontier Research\r\nGrant EP/X033813/1, ERC grant DynAMiCS (101167561) and DFG grant 389792660 as\r\npart of TRR 248. J.O. is also affiliated with Keble College, Oxford as an Emmy Network\r\nfellow." article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Pavol full_name: Kebis, Pavol id: 2e0132b3-4e98-11ef-b275-cf7281c2802a last_name: Kebis - first_name: FLORIAN full_name: LUCA, FLORIAN last_name: LUCA - first_name: JOEL full_name: OUAKNINE, JOEL last_name: OUAKNINE - first_name: ANDREW full_name: SCOONES, ANDREW last_name: SCOONES - first_name: JAMES full_name: WORRELL, JAMES last_name: WORRELL citation: ama: Kebis P, LUCA F, OUAKNINE J, SCOONES A, WORRELL J. Transcendence for Pisot morphic words over an algebraic base. Ergodic Theory and Dynamical Systems. 2026:1-22. doi:10.1017/etds.2026.10324 apa: Kebis, P., LUCA, F., OUAKNINE, J., SCOONES, A., & WORRELL, J. (2026). Transcendence for Pisot morphic words over an algebraic base. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2026.10324 chicago: Kebis, Pavol, FLORIAN LUCA, JOEL OUAKNINE, ANDREW SCOONES, and JAMES WORRELL. “Transcendence for Pisot Morphic Words over an Algebraic Base.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2026. https://doi.org/10.1017/etds.2026.10324. ieee: P. Kebis, F. LUCA, J. OUAKNINE, A. SCOONES, and J. WORRELL, “Transcendence for Pisot morphic words over an algebraic base,” Ergodic Theory and Dynamical Systems. Cambridge University Press, pp. 1–22, 2026. ista: Kebis P, LUCA F, OUAKNINE J, SCOONES A, WORRELL J. 2026. Transcendence for Pisot morphic words over an algebraic base. Ergodic Theory and Dynamical Systems., 1–22. mla: Kebis, Pavol, et al. “Transcendence for Pisot Morphic Words over an Algebraic Base.” Ergodic Theory and Dynamical Systems, Cambridge University Press, 2026, pp. 1–22, doi:10.1017/etds.2026.10324. short: P. Kebis, F. LUCA, J. OUAKNINE, A. SCOONES, J. WORRELL, Ergodic Theory and Dynamical Systems (2026) 1–22. das_tickbox: '0' date_created: 2026-07-27T05:53:25Z date_published: 2026-07-10T00:00:00Z date_updated: 2026-08-03T06:17:50Z day: '10' ddc: - '000' department: - _id: ToHe - _id: GradSch doi: 10.1017/etds.2026.10324 external_id: arxiv: - '2405.05279' fulldoi: https://doi.org/10.1017/etds.2026.10324 has_accepted_license: '1' keyword: - balanced-pair algorithm - Cobham’s conjecture - k-Bonacci words - Pisot conjecture - subspace theorem language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/etds.2026.10324 mathsc: - 11J81 - 37B10 - 11J87 month: '07' oa: 1 oa_version: Published Version page: 1-22 publication: Ergodic Theory and Dynamical Systems publication_identifier: eissn: - 1469-4417 issn: - 0143-3857 publication_status: epub_ahead publisher: Cambridge University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Transcendence for Pisot morphic words over an algebraic base 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 year: '2026' ... --- OA_place: repository OA_type: green _id: '22619' abstract: - lang: eng text: Planar germanium is currently the only semiconducting platform where high-coherence spin qubits and proximity-induced superconductivity have each been demonstrated. Recent research into spin qubits in Ge/SiGe heterostructures has focused on increasing the thickness of the SiGe capping layer, reporting improvements in the electrostatic noise levels. Meanwhile, heterostructures with thinner capping layers remain rather unexplored, despite the potential advantages for proximity-induced superconductivity. Here, we study a Ge/SiGe heterostructure with a thin SiGe cap d - 4nm and investigate its viability to host low-noise quantum dots. To keep the thermal budget compatible with superconducting layers, low-temperature oxide deposition processes were developed and implemented for the gate dielectrics. The charge noise level of the fabricated devices is estimated to be 1.8  +- 1.0 μeV/ square HZ⁠, comparable to devices fabricated on shallow heterostructures (⁠ d - 20nm⁠) with high-temperature deposited oxides. Low charge noise levels, together with the straightforward integration of superconductors, make this heterostructure an attractive platform for prototyping hybrid semiconducting–superconducting devices. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: 'We sincerely thank Nick van Loo, Greg Mazur, Dhananjay Joshi, and Srijit Goswami for their inputs on low-temperature HfOx deposition; Matias Urdampilleta and Daniel Jirovec for discussions; and Kristen Léonard for the careful reading of the manuscript. This research was supported by the Scientific Service Units of ISTA through resources provided by the Miba Machine Shop and the Nanofabrication facility. The authors acknowledge support from the NOMIS Foundation; the European Innovation Council Pathfinder Grant No. 101115315 (QuKiT); the FWF Projects with DOI:10.55776/F86, DOI:10.55776/PAT7682124, and DOI:10.55776/P36507; and the HE-MSCA-PF project with DOI:10.3030/101150858. ICN2 is supported by the Severo Ochoa Program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Program/Generalitat de Catalunya. ICN2 acknowledges funding from Generalitat de Catalunya (No. 2021SGR00457). We acknowledge support from the CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+).' article_number: '033505' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Maksim full_name: Borovkov, Maksim id: 1fd0975f-8b61-11ed-b69e-d149334f28c5 last_name: Borovkov - first_name: Yona A full_name: Schell, Yona A id: fe39122d-06bb-11ec-a33b-9e22b40e40a5 last_name: Schell - first_name: Dina full_name: Sokolova, Dina id: 2d2d62f8-72f0-11ef-b75a-8ec3e8a60032 last_name: Sokolova - first_name: Kevin Etienne Robert full_name: Roux, Kevin Etienne Robert id: 53f93ea2-803f-11ed-ab7e-b283135794ef last_name: Roux - first_name: Paul full_name: Falthansl-Scheinecker, Paul id: 85b43b21-15b2-11ec-abd3-e2c252cc2285 last_name: Falthansl-Scheinecker - first_name: Giorgio full_name: Fabris, Giorgio id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352 last_name: Fabris - first_name: Devashish C full_name: Shah, Devashish C id: de191434-4e7e-11ef-bf4b-9a056fc19fc3 last_name: Shah orcid: 0009-0007-5829-7707 - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo - first_name: Rodolfo full_name: Previdi, Rodolfo id: bc4ea1dc-00ce-11ec-8a4e-b325ca8b9876 last_name: Previdi - first_name: Inas full_name: Taha, Inas last_name: Taha - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Afonso De Cerdeira full_name: Oliveira, Afonso De Cerdeira last_name: Oliveira - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Anton full_name: Bubis, Anton id: 1f6212b5-f795-11ec-9c0c-de4780302890 last_name: Bubis - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Borovkov M, Schell YA, Sokolova D, et al. Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices. Applied Physics Letters. 2026;129(3). doi:10.1063/5.0333142 apa: Borovkov, M., Schell, Y. A., Sokolova, D., Roux, K. E. R., Falthansl-Scheinecker, P., Fabris, G., … Katsaros, G. (2026). Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices. Applied Physics Letters. AIP Publishing. https://doi.org/10.1063/5.0333142 chicago: Borovkov, Maksim, Yona A Schell, Dina Sokolova, Kevin Etienne Robert Roux, Paul Falthansl-Scheinecker, Giorgio Fabris, Devashish C Shah, et al. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices.” Applied Physics Letters. AIP Publishing, 2026. https://doi.org/10.1063/5.0333142. ieee: M. Borovkov et al., “Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices,” Applied Physics Letters, vol. 129, no. 3. AIP Publishing, 2026. ista: Borovkov M, Schell YA, Sokolova D, Roux KER, Falthansl-Scheinecker P, Fabris G, Shah DC, Saez Mollejo J, Previdi R, Taha I, Genç A, Arbiol J, Calcaterra S, Oliveira ADC, Chrastina D, Isella G, Bubis A, Katsaros G. 2026. Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices. Applied Physics Letters. 129(3), 033505. mla: Borovkov, Maksim, et al. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices.” Applied Physics Letters, vol. 129, no. 3, 033505, AIP Publishing, 2026, doi:10.1063/5.0333142. short: M. Borovkov, Y.A. Schell, D. Sokolova, K.E.R. Roux, P. Falthansl-Scheinecker, G. Fabris, D.C. Shah, J. Saez Mollejo, R. Previdi, I. Taha, A. Genç, J. Arbiol, S. Calcaterra, A.D.C. Oliveira, D. Chrastina, G. Isella, A. Bubis, G. Katsaros, Applied Physics Letters 129 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The data that support the findings of this study are openly available in Institute of Science and Technology repository at http://doi.org/10.15479/AT-ISTA-22242, Ref. 50. date_created: 2026-08-02T22:01:53Z date_published: 2026-07-20T00:00:00Z date_updated: 2026-08-03T11:08:39Z day: '20' department: - _id: GeKa - _id: GradSch - _id: NanoFab doi: 10.1063/5.0333142 external_id: arxiv: - '2602.21363' fulldoi: https://doi.org/10.1063/5.0333142 intvolume: ' 129' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2602.21363 month: '07' oa: 1 oa_version: Preprint project: - _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811 grant_number: '101115315' name: Quantum bits with Kitaev Transmons - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: 5b9e579c-ab3d-11f0-914f-88754c5b5a3f grant_number: PAT 7682124 name: Superconducting spin qubits in planar Ge - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3 grant_number: '101150858' name: Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium publication: Applied Physics Letters publication_identifier: eissn: - 1077-3118 issn: - 0003-6951 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: record: - id: '22242' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '22618' abstract: - lang: eng text: "We use a function field version of the circle method to prove that a positive proportion of elements in \U0001D53D\U0001D45E⁡[\U0001D461] are representable as a sum of three cubes of minimal degree from \U0001D53D\U0001D45E⁡[\U0001D461], assuming a suitable form of the Ratios Conjecture and that char⁡(\U0001D53D\U0001D45E) >3. The analogue of this conjecture for quadratic Dirichlet L-functions is known for large fixed q, via recent developments in homological stability." acknowledgement: While working on this paper the first two authors were supported by FWF grant (DOI 10.55776/P36278) and the third author was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413, and by the National Science and Technology Council Project Grant 114-2115-M-001-010-MY2. article_number: e112 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Jakob full_name: Glas, Jakob id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb last_name: Glas - first_name: Victor full_name: Wang, Victor id: 76096395-aea4-11ed-a680-ab8ebbd3f1b9 last_name: Wang orcid: 0000-0002-0704-7026 citation: ama: Browning TD, Glas J, Wang V. Sums of three cubes over a function field. Forum of Mathematics Sigma. 2026;14. doi:10.1017/fms.2026.10259 apa: Browning, T. D., Glas, J., & Wang, V. (2026). Sums of three cubes over a function field. Forum of Mathematics Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2026.10259 chicago: Browning, Timothy D, Jakob Glas, and Victor Wang. “Sums of Three Cubes over a Function Field.” Forum of Mathematics Sigma. Cambridge University Press, 2026. https://doi.org/10.1017/fms.2026.10259. ieee: T. D. Browning, J. Glas, and V. Wang, “Sums of three cubes over a function field,” Forum of Mathematics Sigma, vol. 14. Cambridge University Press, 2026. ista: Browning TD, Glas J, Wang V. 2026. Sums of three cubes over a function field. Forum of Mathematics Sigma. 14, e112. mla: Browning, Timothy D., et al. “Sums of Three Cubes over a Function Field.” Forum of Mathematics Sigma, vol. 14, e112, Cambridge University Press, 2026, doi:10.1017/fms.2026.10259. short: T.D. Browning, J. Glas, V. Wang, Forum of Mathematics Sigma 14 (2026). corr_author: '1' das_tickbox: '0' date_created: 2026-08-02T22:01:52Z date_published: 2026-07-22T00:00:00Z date_updated: 2026-08-03T12:13:59Z day: '22' ddc: - '500' department: - _id: TiBr - _id: GradSch doi: 10.1017/fms.2026.10259 ec_funded: 1 external_id: arxiv: - '2402.07146' file: - access_level: open_access checksum: e92a762e03f832bdca8c106a9a88ef9b content_type: application/pdf creator: dernst date_created: 2026-08-03T12:12:03Z date_updated: 2026-08-03T12:12:03Z file_id: '22636' file_name: 2026_ForumMathematics_Browning.pdf file_size: 810718 relation: main_file success: 1 file_date_updated: 2026-08-03T12:12:03Z fulldoi: https://doi.org/10.1017/fms.2026.10259 has_accepted_license: '1' intvolume: ' 14' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Forum of Mathematics Sigma publication_identifier: eissn: - 2050-5094 publication_status: published publisher: Cambridge University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Sums of three cubes over a function field 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: 14 year: '2026' ... --- OA_place: repository _id: '22242' abstract: - lang: eng text: This deposit contains the data and analysis code accompanying the publication "Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices" (Borovkov et al.). The deposit includes the raw transport and current-noise measurements of three gate-defined quantum-dot devices as QCodes SQLite databases, the master table of the charge-noise (flank-method) analysis with the pointers linking every analyzed PSD trace to the raw data, the toy-model noise simulation datasets behind the supplementary figures, the archived analysis figures (PSD fits and lever-arm extractions), and the Python code reproducing the full analysis and all figures. The code is also maintained at https://github.com/ISTA-Nanoelectronics/noise_paper_public; instructions are provided in the README files. acknowledged_ssus: - _id: M-Shop - _id: NanoFab article_processing_charge: No author: - first_name: Maksim full_name: Borovkov, Maksim id: 1fd0975f-8b61-11ed-b69e-d149334f28c5 last_name: Borovkov citation: ama: Borovkov M. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. 2026. doi:10.15479/AT-ISTA-22242 apa: Borovkov, M. (2026). Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22242 chicago: Borovkov, Maksim. “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22242. ieee: M. Borovkov, “Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices.” Institute of Science and Technology Austria, 2026. ista: Borovkov M. 2026. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices, Institute of Science and Technology Austria, 10.15479/AT-ISTA-22242. mla: Borovkov, Maksim. Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22242. short: M. Borovkov, (2026). contributor: - contributor_type: contact_person first_name: Maksim id: 1fd0975f-8b61-11ed-b69e-d149334f28c5 last_name: Borovkov corr_author: '1' date_created: 2026-07-04T17:32:27Z date_published: 2026-07-04T00:00:00Z date_updated: 2026-08-03T11:08:38Z day: '04' ddc: - '530' department: - _id: GradSch - _id: GeKa doi: 10.15479/AT-ISTA-22242 doi_confirm: '1' file: - access_level: open_access checksum: 2a1ea297e01a7a202a6b144d69a46eef content_type: application/x-zip-compressed creator: mborovko date_created: 2026-07-04T17:28:49Z date_updated: 2026-07-04T17:28:49Z file_id: '22243' file_name: noise_paper_public_deposit.zip file_size: 3082596099 relation: main_file success: 1 file_date_updated: 2026-07-04T17:28:49Z fulldoi: https://doi.org/10.15479/AT-ISTA-22242 has_accepted_license: '1' month: '07' oa: 1 oa_version: Published Version project: - _id: bdc2ca30-d553-11ed-ba76-cf164a5bb811 grant_number: '101115315' name: Quantum bits with Kitaev Transmons - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3 grant_number: '101150858' name: Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium - _id: 5b9e579c-ab3d-11f0-914f-88754c5b5a3f grant_number: PAT 7682124 name: Superconducting spin qubits in planar Ge publisher: Institute of Science and Technology Austria related_material: link: - relation: research_data url: https://github.com/ISTA-Nanoelectronics/noise_paper_public record: - id: '22619' relation: used_in_publication status: public status: public title: Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices 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: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22645' abstract: - lang: eng text: Nanocrystal superlattices are commonly formed by changing concentration, solvent conditions, or particle surface chemistry. Although effective, these approaches alter multiple contributions to the interparticle potential simultaneously, making it difficult to isolate the interactions responsible for ordering or to control assembly in chemically complex environments. Here, we show that oligomeric species present in a nanocrystal reaction medium drive superlattice formation through a depletion mechanism. Using PbTe nanocrystals as a model system, we identify Pb–oleate oligomers in the crude reaction mixture, characterize their solution structure, and quantify their contribution to the interparticle potential, establishing depletion as the dominant short-range interaction governing spontaneous body-centered cubic superlattice formation. We then confirm the depletion origin of ordering by showing that varying depletant concentration predictably shifts the order–disorder boundary and produces a thermally reversible transition between dispersed and ordered states ─ behavior that is inconsistent with van der Waals or ligand-mediated mechanisms but is a direct consequence of depletion control. Having established and validated the mechanism, we demonstrate that the same depletion framework can be deliberately activated in purified dispersions and transferred across nanocrystal systems of different composition and shape, including anisotropic and binary assemblies. These results establish precursor-derived depletion as a general and chemically grounded mechanism for nanocrystal superlattice formation, and show that collective ordering can be programmed through the surrounding medium rather than through particle surface modification. acknowledged_ssus: - _id: EM-Fac - _id: NMR - _id: LifeSc acknowledgement: ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility, and the Lab Support Facility (LSF). M.E. acknowledges financial support from Deutsche Forschungsgemeinschaft through Collaborative Research Centre 1411. We thank Dr. Tommaso Constanzo and Tobias Kleinhanns for assistance with high-quality electron microscope image acquisition, Dr. Jeonghyun Park for providing NCs, Dr. Mariano Calcabrini for assistance with the NMR study, and Prof. Jonathan De Roo for fruitful discussions. This work benefited from the use of the SasView application, originally developed under NSF award DMR-0520547. SasView contains code developed with funding from the European Union’s Horizon 2020 research and innovation program under the SINE2020 project, grant agreement No. 654000. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Daniel full_name: Balazs, Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - first_name: Aiswarya full_name: Rayaroth Puthiyaveettil, Aiswarya id: 8aceb01b-8972-11ed-ae7b-d5fe53775add last_name: Rayaroth Puthiyaveettil - first_name: Sharona full_name: Horta, Sharona id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc last_name: Horta - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Michael full_name: Engel, Michael last_name: Engel - first_name: Ihor full_name: Cherniukh, Ihor id: d03b62b2-5976-11ef-a8d7-9525504b7895 last_name: Cherniukh - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Lee S, Balazs D, Rayaroth Puthiyaveettil A, et al. Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. 2026;148(29):31245-31252. doi:10.1021/jacs.6c07859 apa: Lee, S., Balazs, D., Rayaroth Puthiyaveettil, A., Horta, S., Goodrich, C. P., Engel, M., … Ibáñez, M. (2026). Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. American Chemical Society. https://doi.org/10.1021/jacs.6c07859 chicago: Lee, Seungho, Daniel Balazs, Aiswarya Rayaroth Puthiyaveettil, Sharona Horta, Carl Peter Goodrich, Michael Engel, Ihor Cherniukh, and Maria Ibáñez. “Reaction Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical Society. American Chemical Society, 2026. https://doi.org/10.1021/jacs.6c07859. ieee: S. Lee et al., “Reaction medium asan architect of nanocrystal superlattices,” Journal of the AmericanChemical Society, vol. 148, no. 29. American Chemical Society, pp. 31245–31252, 2026. ista: Lee S, Balazs D, Rayaroth Puthiyaveettil A, Horta S, Goodrich CP, Engel M, Cherniukh I, Ibáñez M. 2026. Reaction medium asan architect of nanocrystal superlattices. Journal of the AmericanChemical Society. 148(29), 31245–31252. mla: Lee, Seungho, et al. “Reaction Medium Asan Architect of Nanocrystal Superlattices.” Journal of the AmericanChemical Society, vol. 148, no. 29, American Chemical Society, 2026, pp. 31245–52, doi:10.1021/jacs.6c07859. short: S. Lee, D. Balazs, A. Rayaroth Puthiyaveettil, S. Horta, C.P. Goodrich, M. Engel, I. Cherniukh, M. Ibáñez, Journal of the AmericanChemical Society 148 (2026) 31245–31252. corr_author: '1' das_tickbox: '0' date_created: 2026-08-04T06:29:31Z date_published: 2026-07-15T00:00:00Z date_updated: 2026-08-04T06:47:13Z day: '15' ddc: - '540' department: - _id: MaIb - _id: LifeSc - _id: GradSch - _id: CaGo doi: 10.1021/jacs.6c07859 external_id: pmid: - '42532904' file: - access_level: open_access checksum: 063314ae5ac4225ebd4436aa8707d113 content_type: application/pdf creator: dernst date_created: 2026-08-04T06:40:17Z date_updated: 2026-08-04T06:40:17Z file_id: '22646' file_name: 2026_JACS_Lee.pdf file_size: 6564594 relation: main_file success: 1 file_date_updated: 2026-08-04T06:40:17Z fulldoi: https://doi.org/10.1021/jacs.6c07859 has_accepted_license: '1' intvolume: ' 148' issue: '29' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 31245-31252 pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Journal of the AmericanChemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Reaction medium asan architect of nanocrystal superlattices 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: 148 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22642' abstract: - lang: eng text: Continuously operating atom-light interfaces represent a key prerequisite for steady-state quantum sensors and efficient quantum processors. Here, we demonstrate continuous accumulation of sub-Doppler-cooled atoms in a shallow intracavity dipole trap, realizing this regime. The key ingredient is a light-shift manipulation that creates spatially varying cooling parameters, enabling efficient capture and accumulation of atoms within a cavity mode. Demonstrated with rubidium atoms, a continuous flux from a source cell is funneled through the magneto-optical trap into the cavity mode, where the atoms are cooled and maintained below 10µK in steady state without time-sequenced operation. We characterize the resulting continuously maintained ensemble of millions of atoms and its collective coupling to the cavity field, establishing a route toward continuously operated cavity-QED systems and long-duration atomic and hybrid quantum sensors. acknowledgement: "The authors thank Vyacheslav Li for his earlier contributions to the development of the setup utilized in this work.\r\nThis work was supported by the Institute of Science and Technology Austria (ISTA); E.G. was supported by the European Research Council under Grant No. 101087907 (ERC CoG\r\nQuHAMP)." article_number: '023302' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Edward-Fulbright full_name: Gheorghita, Edward-Fulbright id: e664a051-133f-11ed-8f02-a05999ad0822 last_name: Gheorghita - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald orcid: 0000-0002-5869-1604 - first_name: Andrea full_name: Pupić, Andrea id: ef9c50a4-5335-11ef-8b9b-8ce03e6380ed last_name: Pupić - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X citation: ama: Gheorghita E-F, Wald S, Pupić A, Hosten O. Continuous accumulation of cold atoms in an optical cavity. Physical Review A. 2026;114(2). doi:10.1103/71f2-sq4p apa: Gheorghita, E.-F., Wald, S., Pupić, A., & Hosten, O. (2026). Continuous accumulation of cold atoms in an optical cavity. Physical Review A. American Physical Society. https://doi.org/10.1103/71f2-sq4p chicago: Gheorghita, Edward-Fulbright, Sebastian Wald, Andrea Pupić, and Onur Hosten. “Continuous Accumulation of Cold Atoms in an Optical Cavity.” Physical Review A. American Physical Society, 2026. https://doi.org/10.1103/71f2-sq4p. ieee: E.-F. Gheorghita, S. Wald, A. Pupić, and O. Hosten, “Continuous accumulation of cold atoms in an optical cavity,” Physical Review A, vol. 114, no. 2. American Physical Society, 2026. ista: Gheorghita E-F, Wald S, Pupić A, Hosten O. 2026. Continuous accumulation of cold atoms in an optical cavity. Physical Review A. 114(2), 023302. mla: Gheorghita, Edward-Fulbright, et al. “Continuous Accumulation of Cold Atoms in an Optical Cavity.” Physical Review A, vol. 114, no. 2, 023302, American Physical Society, 2026, doi:10.1103/71f2-sq4p. short: E.-F. Gheorghita, S. Wald, A. Pupić, O. Hosten, Physical Review A 114 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "There are no publicly available research data or software\r\nsupporting this manuscript. Requests for further information\r\nor data should be sent to the authors." date_created: 2026-08-04T05:58:23Z date_published: 2026-08-03T00:00:00Z date_updated: 2026-08-04T06:07:20Z day: '03' ddc: - '530' department: - _id: OnHo - _id: GradSch doi: 10.1103/71f2-sq4p external_id: arxiv: - '2512.14528' file: - access_level: open_access checksum: fdecc394b734b56e1b3b151a816bbe14 content_type: application/pdf creator: dernst date_created: 2026-08-04T06:03:14Z date_updated: 2026-08-04T06:03:14Z file_id: '22643' file_name: 2026_PhysicalReviewA_Gheorghita.pdf file_size: 959463 relation: main_file success: 1 file_date_updated: 2026-08-04T06:03:14Z fulldoi: https://doi.org/10.1103/71f2-sq4p has_accepted_license: '1' intvolume: ' 114' issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: bdb2a702-d553-11ed-ba76-f12e3e5a3bc6 grant_number: '101087907' name: 'A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics' publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Continuous accumulation of cold atoms in an optical cavity 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: 114 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '22647' abstract: - lang: eng text: "Within the plant endomembrane system, the vesicle coat protein clathrin localizes to the plasma membrane (PM) and the trans-Golgi Network/early endosome (TGN/EE). While the role of clathrin in endocytosis at the PM is well established, its function at TGN/EE, presumably in late secretion (trafficking from the TGN/EE to the cell surface) or en route to the vacuole, is debated. Similarly debated are potential homeostatic mechanisms balancing the trafficking routes, especially endocytosis and late secretion.\r\nWe address these questions in Arabidopsis thaliana using conditional silencing of CLATHRIN HEAVY CHAIN (CHC), conditional overexpression of the clathrin uncoating factor AUXILIN-LIKE1, and secretory mutants.\r\nCHC silencing interferes with trafficking of cargoes destined for the apoplast and the PM, supporting a function of clathrin in late secretion. The secretory cargoes become abnormally rerouted from the TGN/EE to the vacuole. Unlike CHC silencing, overexpression of AUXILIN-LIKE1 selectively inhibits clathrin-mediated endocytosis while secretion continues normally at early points of induction. Conversely, secretory mutants exhibit a reduced PM recruitment of clathrin, and variably, of the TPLATE endocytic component.\r\nTogether, our data show a role of clathrin in secretion and suggest secretion as a fundamental trafficking process to which endocytosis is adjusted by a weak homeostatic mechanism." acknowledgement: 'The authors wish to acknowledge Dr. Paweł Baster for cloning PIN1-GFP-2/pDONR221, Ms. Aline Monzer and Dr. Mingyue Li for help with CHC protein level evaluation, Dr. Michał Rychłowski for help with confocal microscopy, Prof. Ari Pekka Mähönen for sharing the p1R4-pUBQ10:XVE plasmid, and Prof. Ying Gu for sharing seeds of the sec5 mutant. M.A. would like to thank Dr. Xixi Zhang and Prof. Sebastian Bednarek for inspiring discussions. This work was supported by the Taif University Researchers Supporting Project, TURSP-HC2022/02 to JF and SA and Austrian Science Fund (FWF): I 3630-B25 to JF. Open Access funding provided by Institute of Science and Technology Austria.' article_number: nph.71454 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Adam full_name: Gackowski, Adam last_name: Gackowski - first_name: Ivana full_name: Matijevic, Ivana id: 83c17ce3-15b2-11ec-abd3-f486545870bd last_name: Matijevic - first_name: Saqer S. full_name: Alotaibi, Saqer S. last_name: Alotaibi - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. 2026. doi:10.1111/nph.71454 apa: Adamowski, M., Gackowski, A., Matijevic, I., Alotaibi, S. S., & Friml, J. (2026). The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist. Wiley. https://doi.org/10.1111/nph.71454 chicago: Adamowski, Maciek, Adam Gackowski, Ivana Matijevic, Saqer S. Alotaibi, and Jiří Friml. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71454. ieee: M. Adamowski, A. Gackowski, I. Matijevic, S. S. Alotaibi, and J. Friml, “The role of clathrin in post‐Golgi secretion in plant cells,” New Phytologist. Wiley, 2026. ista: Adamowski M, Gackowski A, Matijevic I, Alotaibi SS, Friml J. 2026. The role of clathrin in post‐Golgi secretion in plant cells. New Phytologist., nph. 71454. mla: Adamowski, Maciek, et al. “The Role of Clathrin in Post‐Golgi Secretion in Plant Cells.” New Phytologist, nph. 71454, Wiley, 2026, doi:10.1111/nph.71454. short: M. Adamowski, A. Gackowski, I. Matijevic, S.S. Alotaibi, J. Friml, New Phytologist (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: 'Original data associated with this study have been deposited in Dataset S1. The accession nos. of A. thaliana genes used in this study are as follows: CHC1 (AT3G11130), CHC2 (AT3G08530), CLC2 (AT2G40060), TPLATE (AT3G01780), AP2A1 (AT5G22770), DRP1C (AT1G14830), GNOM-LIKE1 (AT5G39500), BEN3/BIG2 (AT3G60860), TMK4 (AT3G23750), PIN1 (AT1G73590), AUXILIN-LIKE1 (AT4G12780), AP1M2 (AT1G60780), ECHIDNA (AT1G09330), SEC5A (AT1G76850), SEC5B (AT1G21170), TUB2 (AT5G62690), and PP2AA3 (AT1G13320).' date_created: 2026-08-04T06:48:41Z date_published: 2026-07-20T00:00:00Z date_updated: 2026-08-04T07:58:27Z day: '20' department: - _id: JiFr - _id: MaLo - _id: GradSch doi: 10.1111/nph.71454 external_id: pmid: - '42477503' fulldoi: https://doi.org/10.1111/nph.71454 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nph.71454 month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: epub_ahead publisher: Wiley quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: The role of clathrin in post‐Golgi secretion in plant cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22639' abstract: - lang: eng text: We present an abstract Dyson expansion for perturbations that are merely relatively form-bounded, and apply it to the polaron problem. For a large class of polaron-type models, including the Fröhlich and Nelson models, we prove that the vacuum expectation value of the heat semi-group is a completely monotone function of the square of the total momentum. Consequently, the ground-state energy is a concave function of the square of the momentum, a result recently proved for the Fröhlich model in [14] using a probabilistic approach via Wiener integrals. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). article_number: '87' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Davide full_name: Desio, Davide id: ea10a57b-23f6-11ef-9085-80d8596d52ef last_name: Desio orcid: 0000-0001-9840-3809 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Desio D, Seiringer R. Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. 2026;116(4). doi:10.1007/s11005-026-02107-2 apa: Desio, D., & Seiringer, R. (2026). Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-026-02107-2 chicago: Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations and Applications to the Polaron Problem.” Letters in Mathematical Physics. Springer Nature, 2026. https://doi.org/10.1007/s11005-026-02107-2. ieee: D. Desio and R. Seiringer, “Dyson expansion for form-bounded perturbations and applications to the polaron problem,” Letters in Mathematical Physics, vol. 116, no. 4. Springer Nature, 2026. ista: Desio D, Seiringer R. 2026. Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. 116(4), 87. mla: Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations and Applications to the Polaron Problem.” Letters in Mathematical Physics, vol. 116, no. 4, 87, Springer Nature, 2026, doi:10.1007/s11005-026-02107-2. short: D. Desio, R. Seiringer, Letters in Mathematical Physics 116 (2026). corr_author: '1' das_tickbox: '0' date_created: 2026-08-03T13:21:14Z date_published: 2026-07-17T00:00:00Z date_updated: 2026-08-04T05:57:21Z day: '17' ddc: - '510' department: - _id: RoSe - _id: GradSch doi: 10.1007/s11005-026-02107-2 external_id: arxiv: - '2512.13443' file: - access_level: open_access checksum: 1b90ff7da16b9604d6fe2c6281493456 content_type: application/pdf creator: dernst date_created: 2026-08-04T05:55:58Z date_updated: 2026-08-04T05:55:58Z file_id: '22641' file_name: 2026_LettersMathPhysics_Desio.pdf file_size: 371840 relation: main_file success: 1 file_date_updated: 2026-08-04T05:55:58Z fulldoi: https://doi.org/10.1007/s11005-026-02107-2 has_accepted_license: '1' intvolume: ' 116' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Letters in Mathematical Physics publication_identifier: issn: - 1573-0530 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Dyson expansion for form-bounded perturbations and applications to the polaron problem 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: 116 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22644' abstract: - lang: eng text: "We analyze the average behavior of various arithmetic functions at the values of degree \U0001D451 binary forms ordered by height, with probability 1. This approach yields averaged versions of the Chowla conjecture and the Bateman–Horn conjecture for random binary forms. Furthermore, we show that the rational Hasse principle holds for almost all Châtelet varieties defined by a fixed norm form of degree \U0001D452 and by varying binary forms of fixed degree \U0001D451, provided \U0001D452 divides \U0001D451. This proves an average version of a conjecture of Colliot-Thélène." acknowledgement: I am deeply grateful to my advisor Tim Browning for suggesting this problem and for the many valuable discussions that shaped this work. I would also like to thank Efthymios Sofos, Matteo Verzobio, and Shuntaro Yamagishi for discussions and insights that contributed to this paper. I am also very grateful to the anonymous referee for their careful reading and for the considerable effort they put into improving the manuscript. article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Yijie full_name: Diao, Yijie id: 7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b last_name: Diao orcid: 0000-0002-4989-5330 citation: ama: Diao Y. Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal. 2026:1-34. doi:10.1017/s0017089526101074 apa: Diao, Y. (2026). Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal. Cambridge University Press. https://doi.org/10.1017/s0017089526101074 chicago: Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at Random Binary Forms.” Glasgow Mathematical Journal. Cambridge University Press, 2026. https://doi.org/10.1017/s0017089526101074. ieee: Y. Diao, “Liouville function, von Mangoldt function, and norm forms at random binary forms,” Glasgow Mathematical Journal. Cambridge University Press, pp. 1–34, 2026. ista: Diao Y. 2026. Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal., 1–34. mla: Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at Random Binary Forms.” Glasgow Mathematical Journal, Cambridge University Press, 2026, pp. 1–34, doi:10.1017/s0017089526101074. short: Y. Diao, Glasgow Mathematical Journal (2026) 1–34. corr_author: '1' das_tickbox: '0' date_created: 2026-08-04T06:15:04Z date_published: 2026-07-21T00:00:00Z date_updated: 2026-08-04T06:28:01Z day: '21' ddc: - '500' department: - _id: TiBr - _id: GradSch doi: 10.1017/s0017089526101074 external_id: arxiv: - '2506.18065' fulldoi: https://doi.org/10.1017/s0017089526101074 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/S0017089526101074 mathsc: - 11N32 - 11N37 - 11D57 - 11G35 month: '07' oa: 1 oa_version: Published Version page: 1-34 publication: Glasgow Mathematical Journal publication_identifier: eissn: - 1469-509X issn: - 0017-0895 publication_status: epub_ahead publisher: Cambridge University Press quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Liouville function, von Mangoldt function, and norm forms at random binary forms 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 year: '2026' ... --- OA_place: publisher OA_type: gold _id: '21923' abstract: - lang: eng text: "The appearance of simulated natural phenomena heavily depends on the way surfaces are textured. However, applying texture maps to dynamic deformable surfaces presents a significant challenge, due to ever-shifting differences in length scales involved. When these surfaces move and advect the texture along with them, their final appearance degrades as deformed regions dramatically distort their texture map. Modifications to the texture directly at the pixel level in response to the deformation may introduce ghosting artifacts and look unnatural. In the real world, the appearance of surface details on a deforming material changes through the interplay of physical processes such as rupturing, exposure of internal structure, or wrinkling. Motivated by these behaviors, in this work we explore how physical principles can guide the texturing methods based on the measure of surface deformation.\r\nWe present two novel wave-based procedural texturing algorithms which reproduce common physical properties like advection and self-similarity, enabling the plausible animation of deforming objects with extreme texture map distortions. Our algorithms are fully procedural, require no actual physics simulation, and store no state or history of deformation besides the input UV map, making them highly parallelizable on the GPU and efficient enough for real-time applications. We show the versatility of the method by animating physical phenomena with extreme deformations such as flowing lava, stretching putty and outpouring sludge." acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback. We also thank Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA)." article_number: '154' article_processing_charge: Yes article_type: original author: - first_name: Aleksei full_name: Kalinov, Aleksei id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02 last_name: Kalinov orcid: 0000-0003-2189-3904 - first_name: Mickaël full_name: Ly, Mickaël id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1 last_name: Ly - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 2026;45(4). doi:10.1145/3811353 apa: 'Kalinov, A., Ly, M., Hafner, C., & Wojtan, C. (2026). Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3811353' chicago: Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on Graphics. Association for Computing Machinery, 2026. https://doi.org/10.1145/3811353. ieee: A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural texturing of extremely deformable surfaces,” ACM Transactions on Graphics, vol. 45, no. 4. Association for Computing Machinery, 2026. ista: Kalinov A, Ly M, Hafner C, Wojtan C. 2026. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154. mla: Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” ACM Transactions on Graphics, vol. 45, no. 4, 154, Association for Computing Machinery, 2026, doi:10.1145/3811353. short: A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45 (2026). conference: end_date: 2026-07-23 location: Los Angeles, CA, United States name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques' start_date: 2026-07-19 corr_author: '1' das_tickbox: '0' date_created: 2026-05-29T13:25:16Z date_published: 2026-07-01T00:00:00Z date_updated: 2026-08-04T09:07:44Z day: '01' ddc: - '006' department: - _id: GradSch - _id: ChWo doi: 10.1145/3811353 file: - access_level: open_access checksum: ea165bf731ddd3045f83878dcb833672 content_type: video/mp4 creator: akalinov date_created: 2026-05-29T13:19:33Z date_updated: 2026-05-29T13:19:33Z file_id: '21924' file_name: tog454-article154-supplemental.mp4 file_size: 77337231 relation: main_file success: 1 - access_level: open_access checksum: 6274cfb15ea5ba7324b74afc7b0d9629 content_type: video/mp4 creator: akalinov date_created: 2026-05-29T13:19:37Z date_updated: 2026-05-29T13:19:37Z file_id: '21925' file_name: tog454-article154-video.mp4 file_size: 226633977 relation: main_file success: 1 - access_level: open_access checksum: 9d41b322a7876be9a3311017b9973183 content_type: application/pdf creator: akalinov date_created: 2026-05-29T13:19:33Z date_updated: 2026-05-29T13:19:33Z file_id: '21926' file_name: tog454-article154-supplemental.pdf file_size: 6793867 relation: main_file success: 1 - access_level: open_access checksum: 51bc60d2de867fbfa570652dec7993b4 content_type: application/pdf creator: akalinov date_created: 2026-05-29T13:19:36Z date_updated: 2026-05-29T13:19:36Z file_id: '21927' file_name: tog454-article154-main-1.pdf file_size: 84173392 relation: main_file success: 1 file_date_updated: 2026-05-29T13:19:37Z fulldoi: https://doi.org/10.1145/3811353 has_accepted_license: '1' intvolume: ' 45' issue: '4' keyword: - Procedural animation language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/infinite-deformation-and-shape-computation/ researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Physics-inspired procedural texturing of extremely deformable surfaces 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: 45 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22295' abstract: - lang: eng text: 'Despite the functional diversity of over 100 causal genes1,2,3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD.' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical assistance; A. Stichelberger and S. Liegenfeld for the management of our animal colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance; C. Jansen and the Scientific Computing Facility for bioinformatics support and technical assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted in Fig. 1; and all members of the laboratory of G.N. for their support and discussions. This study was supported by the Scientific Service Units of ISTA through resources provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities, member of the Vienna BioCenter. This work was supported by a European Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lena A full_name: Schwarz, Lena A id: 29A8453C-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Sergey full_name: Isaev, Sergey last_name: Isaev - first_name: Michela full_name: Lisi, Michela id: 39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c last_name: Lisi - first_name: Daniel full_name: Malzl, Daniel last_name: Malzl - first_name: Christoph full_name: Büschl, Christoph id: 2a8c054c-0913-11ee-9159-f8ef515809ed last_name: Büschl - first_name: Sabrina full_name: Ladstätter, Sabrina last_name: Ladstätter - first_name: Bárbara full_name: Oliveira, Bárbara id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87 last_name: Oliveira - first_name: Matteo full_name: Barel, Matteo id: 8959927b-2236-11ed-bd6e-ea83d94ade0e last_name: Barel - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Chaitanya full_name: Chintaluri, Chaitanya id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E last_name: Chintaluri orcid: 0000-0003-4252-1608 - first_name: Sarah full_name: Gorkiewicz, Sarah id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f last_name: Gorkiewicz - first_name: Mohammad full_name: Goudarzi, Mohammad id: 3384113A-F248-11E8-B48F-1D18A9856A87 last_name: Goudarzi - first_name: Tereza full_name: Belinova, Tereza id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368 last_name: Belinova - first_name: Stephan full_name: Reichl, Stephan last_name: Reichl - first_name: Gintarė full_name: Sendžikaitė, Gintarė id: dd6d52f2-c50d-11eb-9548-bcf0ff82b344 last_name: Sendžikaitė - first_name: Satish full_name: Arcot Jayaram, Satish id: b0bbee33-09f7-11eb-909c-8b358058d28a last_name: Arcot Jayaram orcid: 0000-0002-2479-2669 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Jörg full_name: Menche, Jörg last_name: Menche - first_name: Igor full_name: Adameyko, Igor last_name: Adameyko - first_name: Peter Vasili full_name: Kharchenko, Peter Vasili id: 0095641e-7eb7-11f1-8665-aec51a2ab5e0 last_name: Kharchenko - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across autism spectrum disorder mouse models. Nature. 2026. doi:10.1038/s41586-026-10679-1 apa: Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino, G. (2026). Cortical development dynamics across autism spectrum disorder mouse models. Nature. Springer Nature. https://doi.org/10.1038/s41586-026-10679-1 chicago: Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl, Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” Nature. Springer Nature, 2026. https://doi.org/10.1038/s41586-026-10679-1. ieee: L. A. Schwarz et al., “Cortical development dynamics across autism spectrum disorder mouse models,” Nature. Springer Nature, 2026. ista: Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics across autism spectrum disorder mouse models. Nature. mla: Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” Nature, Springer Nature, 2026, doi:10.1038/s41586-026-10679-1. short: L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter, B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi, T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M. Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino, Nature (2026). corr_author: '1' dataavailabilitystatement: Single-nucleus multiomics data are available from the Gene Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz). Source data are provided with this paper. Scripts and analyses that support the main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome). date_created: 2026-07-13T09:47:21Z date_published: 2026-06-17T00:00:00Z date_updated: 2026-08-04T09:29:55Z day: '17' ddc: - '570' department: - _id: AnKi - _id: GaNo - _id: TiVo - _id: ScienComp - _id: GradSch - _id: Bio - _id: PreCl doi: 10.1038/s41586-026-10679-1 external_id: pmid: - '42310454' fulldoi: https://doi.org/10.1038/s41586-026-10679-1 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41586-026-10679-1 month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6 grant_number: '101044865' name: Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders - _id: 9B91375C-BA93-11EA-9121-9846C619BF3A grant_number: '707964' name: Critical windows and reversibility of ASD associated with mutations in chromatin remodelers - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets - _id: ebb38b5d-77a9-11ec-83b8-a42e08120a88 grant_number: FG1803 49015 name: Neurobiology of anxiety in autism spectrum disorders publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/patterns-in-genetic-chaos/ researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Cortical development dynamics across autism spectrum disorder mouse models 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 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22268' abstract: - lang: eng text: AlphaFold3 predicts highly accurate protein structures from sequence but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover, its predictions are oblivious to experimental conditions that can alter local sequence conformation. In this work, we show that AlphaFold3 can be guided to match data obtained by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and cryogenic electron microscopy (cryo-EM) experiments and combinations thereof. Our approach can also incorporate data that explicitly report on dynamics, such as site-resolved order parameters. We demonstrate that this methodology generates compact structural ensembles whose ensemble-averaged observables agree with experiment, with fewer distance restraint violations than traditionally resolved NMR structures and with unmodeled alternate conformations uncovered in electron density. This methodology paves the way for experimentally aware predictive models that generate structural ensembles consistent with the measurements, potentially over multiple modalities, and that can be further refined toward thermodynamically grounded ensembles by incorporating energetics. acknowledgement: A. Marx acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. A.M.B. and P.S. are supported by the Institute of Science and Technology Austria Internal Project Call grant Generative Protein NMR. S.V. was supported in part by funding from the Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sai A full_name: Maddipatla, Sai A id: e957f5e5-91c9-11f0-a95f-e090f66ecb4d last_name: Maddipatla - first_name: Nadav E full_name: Sellam, Nadav E id: ef280fe0-91c9-11f0-a95f-8dea3f5bc513 last_name: Sellam - first_name: Meital I full_name: Bojan, Meital I id: 11d88cf5-91ca-11f0-a95f-edf9f08f47b7 last_name: Bojan - first_name: Vova full_name: Masalitin, Vova id: ff7958eb-91c9-11f0-a95f-f3bf65828cf6 last_name: Masalitin - first_name: Sanketh full_name: Vedula, Sanketh last_name: Vedula - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Ailie full_name: Marx, Ailie last_name: Marx - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 citation: ama: Maddipatla SA, Sellam NE, Bojan MI, et al. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology. 2026. doi:10.1038/s41587-026-03166-5 apa: Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Masalitin, V., Vedula, S., Schanda, P., … Bronstein, A. M. (2026). Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-026-03166-5 chicago: Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Vova Masalitin, Sanketh Vedula, Paul Schanda, Ailie Marx, and Alex M. Bronstein. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” Nature Biotechnology. Springer Nature, 2026. https://doi.org/10.1038/s41587-026-03166-5. ieee: S. A. Maddipatla et al., “Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles,” Nature Biotechnology. Springer Nature, 2026. ista: Maddipatla SA, Sellam NE, Bojan MI, Masalitin V, Vedula S, Schanda P, Marx A, Bronstein AM. 2026. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology. mla: Maddipatla, Sai A., et al. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” Nature Biotechnology, Springer Nature, 2026, doi:10.1038/s41587-026-03166-5. short: S.A. Maddipatla, N.E. Sellam, M.I. Bojan, V. Masalitin, S. Vedula, P. Schanda, A. Marx, A.M. Bronstein, Nature Biotechnology (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: All structures and metrics reported in this paper are openly available on Harvard Dataverse - https://doi.org/10.7910/DVN/PLYUHN. All code is openly available on GitHub (https://github.com/sai-advaith/guided_alphafold); the version used for this paper (version 0.9.1) is permanently archived on Zenodo https://doi.org/10.5281/zenodo.17307005 date_created: 2026-07-12T22:02:19Z date_published: 2026-06-29T00:00:00Z date_updated: 2026-08-04T09:25:18Z day: '29' ddc: - '570' department: - _id: PaSc - _id: AlBr - _id: GradSch doi: 10.1038/s41587-026-03166-5 external_id: pmid: - '42374114' fulldoi: https://doi.org/10.1038/s41587-026-03166-5 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41587-026-03166-5 month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/toward-experiment-guided-alphafold/ researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles 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 year: '2026' ... --- OA_place: publisher _id: '22334' abstract: - lang: eng text: "Characterizing protein dynamics at the atomic level is essential for our understanding of biological mechanisms. Whether it is to facilitate metabolite transport, catalyze reactions, transmit signals, or regulate metabolism – proteins are constantly in motion and sample multiple conformational states to fulfill their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly well suited to elucidate the dynamics of biomolecules on their complex free-energy landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the study of large molecular assemblies, protein crystals, or insoluble proteins at atomic resolution without an inherent molecular size limitation. MAS NMR experiments to probe protein dynamics are extremely versatile and sensitive to motional timescales from picoseconds to seconds. Over the past decades, technological advances, developments in experimental design, and new isotope-labeling approaches have further expanded the possibilities of this technique and significantly improved the accuracy of the determined motional parameters.\r\nFunctionally important sites of proteins often contain aromatic residues. Their side-chain motions have therefore long served as valuable indicators of mechanistically relevant dynamics in NMR studies. In this thesis, site-specifically labeled aromatic residues act as sensitive reporters for MAS NMR studies of protein dynamics. The first part addresses how different environments impact side-chain motion by probing ring flips of phenylalanines and tyrosines in crystalline proteins and amyloid fibrils. It provides important insights for the analysis of dynamics obtained in non-native protein environments and emphasizes the complex factors that determine the timescale of internal dynamics. In the second part, the focus shifts towards methodological questions regarding the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits promising characteristics for NMR studies but also presents significant challenges, which is why the full methodological potential of 19F MAS NMR has not been fully realized yet. This work demonstrates that paramagnetic doping can considerably reduce the measurement time and improve the sensitivity of fluorinated samples. Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics on the example of tryptophans. The results illustrate the challenges in analyzing such experiments and lay the foundation for further development of 19F MAS NMR relaxation studies.\r\nTaken together, this thesis highlights the potential of combining specific isotope labeling, MAS NMR, and complementary methods such as crystallography and computational simulations to elucidate internal protein dynamics. The further development of such integrative approaches will be crucial to improving our understanding of complex mechanisms and protein function.\r\n" acknowledged_ssus: - _id: LifeSc - _id: NMR acknowledgement: "During the work on this thesis, I was the recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 citation: ama: Becker LM. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. 2026. doi:10.15479/AT-ISTA-22334 apa: Becker, L. M. (2026). Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22334 chicago: Becker, Lea Marie. “Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22334. ieee: L. M. Becker, “Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026. ista: Becker LM. 2026. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria. mla: Becker, Lea Marie. Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22334. short: L.M. Becker, Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '1' date_created: 2026-07-14T08:08:51Z date_published: 2026-07-13T00:00:00Z date_updated: 2026-08-04T09:32:45Z day: '13' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-22334 doi_confirm: '1' file: - access_level: closed checksum: 8b85114eff543916c0e1445cd2189555 content_type: application/zip creator: lbecker date_created: 2026-07-16T09:17:08Z date_updated: 2026-07-16T09:17:08Z file_id: '22346' file_name: 2026_Becker_Lea_source_files.zip file_size: 99472908 relation: source_file - access_level: open_access checksum: 6c526862bc6dbd1e4c80ecb34580bc58 content_type: application/pdf creator: lbecker date_created: 2026-07-16T09:17:05Z date_updated: 2026-07-16T09:17:05Z file_id: '22347' file_name: 2026_Becker_Lea_Thesis.pdf file_size: 74647289 relation: main_file success: 1 file_date_updated: 2026-07-16T09:17:08Z fulldoi: https://doi.org/10.15479/AT-ISTA-22334 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: '205' project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publication_identifier: isbn: - 978-3-99078-084-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12675' relation: part_of_dissertation status: public - id: '21777' relation: part_of_dissertation status: public - id: '12114' relation: part_of_dissertation status: public - id: '22105' relation: part_of_dissertation status: public status: public supervisor: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 title: Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ...