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Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21957","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.","ista":"Zapata J. 2026. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria.","ama":"Zapata J. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. 2026. doi: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.","short":"J. Zapata, Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames, Institute of Science and Technology Austria, 2026."},"ddc":["500"],"das_tickbox":"1","oa_version":"Published Version","type":"dissertation","month":"06","related_material":{"record":[{"id":"21144","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"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.","lang":"eng"}],"day":"09","acknowledgement":"Funding: Vienna Graduate School on Computational Optimization (FWF), grant DOI: 10.55776/W1260.","degree_awarded":"PhD","oa":1,"supervisor":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"year":"2026","language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","date_created":"2026-06-08T13:29:52Z","_id":"21957","page":"89","file_date_updated":"2026-06-10T13:33:25Z","title":"Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames","author":[{"first_name":"Jeferson","last_name":"Zapata","full_name":"Zapata, Jeferson","id":"00223538-AF8F-11E9-A4C7-F729E6697425"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-079-4"]},"doi_confirm":"1","file":[{"file_size":40811933,"content_type":"application/zip","date_updated":"2026-06-08T13:20:02Z","date_created":"2026-06-08T13:20:02Z","file_name":"istaustriathesis_JZapata.zip","relation":"source_file","creator":"jzapata","file_id":"21958","access_level":"closed","checksum":"b11a959e99d3dcf61040282b5c837141"},{"success":1,"checksum":"edf1e5899b2e31505cd1aa3fe8bd4b7f","relation":"main_file","creator":"jzapata","file_id":"21992","access_level":"open_access","file_size":2207892,"content_type":"application/pdf","date_created":"2026-06-10T13:33:25Z","file_name":"4_Final_Thesis_JZapata_REX.pdf","date_updated":"2026-06-10T13:33:25Z"}]},{"article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by-sa/4.0/","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","fulldoi":"https://doi.org/10.15479/AT-ISTA-21360","date_updated":"2026-07-27T14:30:08Z","das_tickbox":"1","oa_version":"Published Version","type":"dissertation","month":"02","related_material":{"record":[{"status":"public","id":"21363","relation":"research_data"}]},"project":[{"grant_number":"101060393","name":"Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks","_id":"34afa094-11ca-11ed-8bc3-a375845a59fb"}],"status":"public","doi":"10.15479/AT-ISTA-21360","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)"},"date_published":"2026-02-26T00:00:00Z","ddc":["570","575","583"],"citation":{"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.","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","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","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.","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.","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.","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."},"supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"year":"2026","OA_place":"repository","corr_author":"1","language":[{"iso":"eng"}],"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). ","degree_awarded":"PhD","day":"26","title":"Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species","author":[{"orcid":"0000-0003-3413-1343","first_name":"Stefan","last_name":"Riegler","full_name":"Riegler, Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425"}],"publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","doi_confirm":"1","file":[{"checksum":"2f1f44e8536c2538f94a440217452c9f","access_level":"closed","file_id":"21386","relation":"source_file","creator":"sriegler","date_created":"2026-03-02T10:59:50Z","file_name":"2026_Riegler_Stefan_Thesis.zip","date_updated":"2026-03-02T10:59:50Z","content_type":"application/x-zip-compressed","file_size":31430022},{"file_size":11635090,"embargo_to":"open_access","content_type":"application/pdf","date_updated":"2026-03-02T10:59:49Z","file_name":"2026_Riegler_Stefan_Thesis.pdf","date_created":"2026-03-02T10:59:49Z","embargo":"2027-02-27","relation":"main_file","creator":"sriegler","file_id":"21387","access_level":"closed","checksum":"2e8dc39640bc26ae5684c944c619719b"}],"file_date_updated":"2026-03-02T10:59:50Z","_id":"21360","date_created":"2026-02-27T09:08:14Z","page":"185"},{"contributor":[{"first_name":"Eva","contributor_type":"supervisor","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"year":"2026","corr_author":"1","day":"27","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","fulldoi":"https://doi.org/10.15479/AT-ISTA-21363","date_updated":"2026-07-27T14:30:07Z","oa_version":"Published Version","title":"Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species","type":"research_data","author":[{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","full_name":"Riegler, Stefan","last_name":"Riegler","first_name":"Stefan","orcid":"0000-0003-3413-1343"}],"publisher":"Institute of Science and Technology Austria","month":"02","file":[{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","embargo_to":"open_access","date_updated":"2026-02-27T09:11:33Z","date_created":"2026-02-27T09:11:33Z","file_name":"SupplementaryTables.xlsx","file_size":63749444,"embargo":"2027-02-27","file_id":"21364","access_level":"closed","relation":"main_file","creator":"sriegler","checksum":"de9145fa166a28c588b5184a2d3d4fee"},{"checksum":"ce1f163551c96cee45943a8ea29720b6","creator":"sriegler","relation":"main_file","file_id":"21365","access_level":"closed","embargo":"2027-02-27","file_size":124,"content_type":"text/plain","embargo_to":"open_access","file_name":"ReadMe.txt","date_created":"2026-02-27T09:13:11Z","date_updated":"2026-02-27T09:13:11Z"}],"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."}],"related_material":{"record":[{"status":"public","id":"21360","relation":"used_in_publication"}]},"status":"public","doi":"10.15479/AT-ISTA-21363","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)"},"date_published":"2026-02-27T00:00:00Z","file_date_updated":"2026-02-27T09:13:11Z","citation":{"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","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).","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.","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.","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.","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"},"ddc":["575"],"date_created":"2026-02-27T09:18:41Z","_id":"21363"},{"das_tickbox":"1","oa_version":"Published Version","external_id":{"pmid":["42223342"],"chemrxivid":["10.26434/chemrxiv.15001696"]},"type":"journal_article","month":"06","abstract":[{"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.","lang":"eng"}],"status":"public","doi":"10.1021/acs.nanolett.6c01462","OA_type":"hybrid","date_published":"2026-06-01T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"ddc":["540"],"citation":{"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","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.","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.","short":"A. Gulyaev, J. Hazarika, Z.-F. Liu, L. Venkataraman, Nano Letters 26 (2026) 7429–7434.","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","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.","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."},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","department":[{"_id":"LaVe"},{"_id":"GradSch"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"22","publication_status":"published","fulldoi":"https://doi.org/10.1021/acs.nanolett.6c01462","date_updated":"2026-07-28T09:57:28Z","title":"A computationally efficient and accurate method for predicting conductance of single-molecule junctions","quality_controlled":"1","chemrxivid":1,"article_type":"letter_note","author":[{"first_name":"Artem","full_name":"Gulyaev, Artem","id":"83ed7901-7380-11f0-bf20-a0788d5e654d","last_name":"Gulyaev"},{"first_name":"Jyotisman","orcid":"0009-0007-2542-7878","full_name":"Hazarika, Jyotisman","last_name":"Hazarika","id":"d87714c4-663d-11f0-bd06-caece19833e5"},{"first_name":"Zhen-Fei","full_name":"Liu, Zhen-Fei","last_name":"Liu"},{"first_name":"Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","last_name":"Venkataraman"}],"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publisher":"American Chemical Society","file":[{"success":1,"checksum":"897551374cac28e0db26dcb0b676b8e7","creator":"dernst","relation":"main_file","file_id":"22013","access_level":"open_access","file_size":3362800,"content_type":"application/pdf","date_updated":"2026-06-16T09:11:35Z","date_created":"2026-06-16T09:11:35Z","file_name":"2026_NanoLetters_Gulyaev.pdf"}],"scopus_import":"1","file_date_updated":"2026-06-16T09:11:35Z","_id":"21980","page":"7429–7434","date_created":"2026-06-10T07:27:19Z","oa":1,"intvolume":" 26","year":"2026","corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"PlanS_conform":"1","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.","day":"01","publication":"Nano Letters","volume":26},{"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.","arxiv":1,"day":"01","publication":"Letters in Mathematical Physics","volume":116,"intvolume":" 116","oa":1,"OA_place":"repository","mathsc":["81V70"],"language":[{"iso":"eng"}],"year":"2026","supplementarymaterial":"no","date_created":"2026-07-26T22:01:40Z","_id":"22404","author":[{"last_name":"Marcelli","full_name":"Marcelli, Giovanna","first_name":"Giovanna"},{"first_name":"Lorenzo","last_name":"Pigozzi","full_name":"Pigozzi, Lorenzo","id":"efb8f850-3208-11ee-ac71-8c4f5803b9c6"},{"last_name":"Porta","full_name":"Porta, Marcello","first_name":"Marcello"}],"article_type":"original","title":"Longitudinal conductivity at integer quantum Hall transitions","quality_controlled":"1","scopus_import":"1","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"publisher":"Springer Nature","issue":"4","publication_status":"published","fulldoi":"https://doi.org/10.1007/s11005-026-02087-3","date_updated":"2026-07-29T10:51:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"not applicable","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"article_processing_charge":"No","article_number":"82","dataavailabilitystatement":"Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.","doi":"10.1007/s11005-026-02087-3","OA_type":"green","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2503.01381"}],"citation":{"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.","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","short":"G. Marcelli, L. Pigozzi, M. Porta, Letters in Mathematical Physics 116 (2026).","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.","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","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."},"date_published":"2026-08-01T00:00:00Z","external_id":{"arxiv":["2503.01381"]},"type":"journal_article","das_tickbox":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"08"},{"researchdata_availability":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.46298/afm.14253","date_updated":"2026-07-29T10:50:17Z","publication_status":"published","keyword":["Farkas lemma","linear programming","extended reals","calculus of inductive constructions"],"article_number":"14253","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"VlKo"},{"_id":"GradSch"}],"date_published":"2026-03-13T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"ddc":["500"],"citation":{"short":"M. Dvorak, V. Kolmogorov, Annals of Formalized Mathematics 2 (2026).","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.","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","ista":"Dvorak M, Kolmogorov V. 2026. Duality theory in linear optimization and its extensions -- formally verified. Annals of Formalized Mathematics. 2, 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.","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.","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"},"status":"public","OA_type":"hybrid","doi":"10.46298/afm.14253","month":"03","related_material":{"record":[{"id":"20071","status":"public","relation":"earlier_version"}]},"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"}],"das_tickbox":"0","oa_version":"Published Version","type":"journal_article","external_id":{"arxiv":["2409.08119"]},"volume":2,"publication":"Annals of Formalized Mathematics","PlanS_conform":"1","day":"13","arxiv":1,"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.","year":"2026","mathsc":["68V20","15A39","90C05"],"language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","intvolume":" 2","_id":"22607","date_created":"2026-07-29T09:06:55Z","supplementarymaterial":"no","publisher":"EPI Sciences","publication_identifier":{"eissn":["3117-4604"]},"quality_controlled":"1","title":"Duality theory in linear optimization and its extensions -- formally verified","article_type":"original","author":[{"first_name":"Martin","orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"},{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}]},{"file":[{"file_size":1771231,"file_name":"2026_Dvorak_Martin_Thesis.pdf","date_updated":"2026-03-04T08:56:15Z","date_created":"2026-03-04T08:56:15Z","content_type":"application/pdf","relation":"main_file","creator":"mdvorak","access_level":"open_access","file_id":"21394","checksum":"cface6dc18152680962b5361575f6e4f","success":1},{"file_size":864585,"date_updated":"2026-03-04T09:03:37Z","file_name":"2026_Dvorak_Martin_Thesis.docx","date_created":"2026-03-04T09:03:37Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"290ddfacfb7e07fb07e6f0b334e67c90","creator":"mdvorak","relation":"source_file","access_level":"closed","file_id":"21395"}],"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-074-9"]},"author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","last_name":"Dvorak","full_name":"Dvorak, Martin","first_name":"Martin","orcid":"0000-0001-5293-214X"}],"title":"Pursuit of truth and beauty in Lean 4: Formally verified theory of grammars, optimization, matroids","_id":"21393","page":"160","date_created":"2026-03-04T09:26:46Z","file_date_updated":"2026-03-04T09:03:37Z","language":[{"iso":"eng"}],"corr_author":"1","OA_place":"repository","year":"2026","oa":1,"supervisor":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jasmin","last_name":"Blanchette","full_name":"Blanchette, Jasmin"}],"day":"04","degree_awarded":"PhD","abstract":[{"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.","lang":"eng"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/madvorak/duality/tree/v3.5.0","description":"Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality)"},{"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)","url":"https://github.com/madvorak/chomsky/tree/v1.2.0","relation":"software"},{"relation":"software","url":"https://github.com/madvorak/grammars","description":"Old version (Lean 3) of the project about grammars"},{"relation":"software","url":"https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean","description":"Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis"}],"record":[{"status":"public","id":"13120","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"20071"},{"id":"21398","status":"public","relation":"part_of_dissertation"}]},"month":"03","type":"dissertation","oa_version":"Published Version","citation":{"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.","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","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.","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.","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.","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.","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"},"ddc":["511","000"],"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2026-03-04T00:00:00Z","doi":"10.15479/AT-ISTA-21393","status":"public","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-21393","date_updated":"2026-07-29T12:56:52Z","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"quality_controlled":"1","title":"Transcendence for Pisot morphic words over an algebraic base","author":[{"last_name":"Kebis","full_name":"Kebis, Pavol","id":"2e0132b3-4e98-11ef-b275-cf7281c2802a","first_name":"Pavol"},{"first_name":"FLORIAN","full_name":"LUCA, FLORIAN","last_name":"LUCA"},{"full_name":"OUAKNINE, JOEL","last_name":"OUAKNINE","first_name":"JOEL"},{"last_name":"SCOONES","full_name":"SCOONES, ANDREW","first_name":"ANDREW"},{"full_name":"WORRELL, JAMES","last_name":"WORRELL","first_name":"JAMES"}],"article_type":"original","publisher":"Cambridge University Press","publication_identifier":{"issn":["0143-3857"],"eissn":["1469-4417"]},"scopus_import":"1","supplementarymaterial":"no","_id":"22406","page":"1-22","date_created":"2026-07-27T05:53:25Z","oa":1,"year":"2026","language":[{"iso":"eng"}],"mathsc":["11J81","37B10","11J87"],"OA_place":"publisher","PlanS_conform":"1","arxiv":1,"day":"10","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.","publication":"Ergodic Theory and Dynamical Systems","oa_version":"Published Version","das_tickbox":"0","external_id":{"arxiv":["2405.05279"]},"type":"journal_article","month":"07","abstract":[{"lang":"eng","text":"It is known that for a uniform morphic sequence 𝒖 =⟨𝑢𝑛⟩∞\r\n𝑛=0 and an algebraic number 𝛽 such that |𝛽| >1, the number [[𝒖]]𝛽 :=∑∞\r\n𝑛=0(𝑢𝑛/𝛽𝑛) either lies in ℚ(𝛽) 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 [[𝒖]]𝛽 outright. In particular, for 𝑘 ≥2, if 𝒖 is the k-Bonacci word, then [[𝒖]]𝛽 is transcendental."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/etds.2026.10324"}],"status":"public","OA_type":"hybrid","doi":"10.1017/etds.2026.10324","date_published":"2026-07-10T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"citation":{"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","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.","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.","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","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.","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."},"ddc":["000"],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"keyword":["balanced-pair algorithm","Cobham’s conjecture","k-Bonacci words","Pisot conjecture","subspace theorem"],"researchdata_availability":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-03T06:17:50Z","fulldoi":"https://doi.org/10.1017/etds.2026.10324","publication_status":"epub_ahead"},{"article_processing_charge":"No","department":[{"_id":"GeKa"},{"_id":"GradSch"},{"_id":"NanoFab"}],"article_number":"033505","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"yes","issue":"3","publication_status":"published","fulldoi":"https://doi.org/10.1063/5.0333142","date_updated":"2026-08-03T11:08:39Z","das_tickbox":"1","oa_version":"Preprint","external_id":{"arxiv":["2602.21363"]},"type":"journal_article","month":"07","related_material":{"record":[{"relation":"research_data","status":"public","id":"22242"}]},"abstract":[{"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.","lang":"eng"}],"project":[{"grant_number":"101115315","name":"Quantum bits with Kitaev Transmons","_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811"},{"grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"name":"Superconducting spin qubits in planar Ge","grant_number":"PAT 7682124","_id":"5b9e579c-ab3d-11f0-914f-88754c5b5a3f"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507"},{"_id":"8ea8abf7-16d5-11f0-9cad-c41e56ec8bb3","grant_number":"101150858","name":"Realization and Manipulation of a Planar hybrid superconducting Andreev spin qubit in Germanium"}],"status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2602.21363","open_access":"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.","doi":"10.1063/5.0333142","OA_type":"green","date_published":"2026-07-20T00:00:00Z","citation":{"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.","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","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.","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).","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.","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.","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"},"oa":1,"intvolume":" 129","year":"2026","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"OA_place":"repository","corr_author":"1","language":[{"iso":"eng"}],"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+).","day":"20","arxiv":1,"volume":129,"publication":"Applied Physics Letters","title":"Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices","quality_controlled":"1","author":[{"full_name":"Borovkov, Maksim","last_name":"Borovkov","id":"1fd0975f-8b61-11ed-b69e-d149334f28c5","first_name":"Maksim"},{"id":"fe39122d-06bb-11ec-a33b-9e22b40e40a5","full_name":"Schell, Yona A","last_name":"Schell","first_name":"Yona A"},{"first_name":"Dina","id":"2d2d62f8-72f0-11ef-b75a-8ec3e8a60032","last_name":"Sokolova","full_name":"Sokolova, Dina"},{"id":"53f93ea2-803f-11ed-ab7e-b283135794ef","full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","first_name":"Kevin Etienne Robert"},{"first_name":"Paul","last_name":"Falthansl-Scheinecker","full_name":"Falthansl-Scheinecker, Paul","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285"},{"first_name":"Giorgio","last_name":"Fabris","full_name":"Fabris, Giorgio","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352"},{"id":"de191434-4e7e-11ef-bf4b-9a056fc19fc3","full_name":"Shah, Devashish C","last_name":"Shah","orcid":"0009-0007-5829-7707","first_name":"Devashish C"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo","first_name":"Jaime"},{"id":"bc4ea1dc-00ce-11ec-8a4e-b325ca8b9876","full_name":"Previdi, Rodolfo","last_name":"Previdi","first_name":"Rodolfo"},{"first_name":"Inas","last_name":"Taha","full_name":"Taha, Inas"},{"last_name":"Genç","full_name":"Genç, Aziz","first_name":"Aziz"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Calcaterra","full_name":"Calcaterra, Stefano","first_name":"Stefano"},{"first_name":"Afonso De Cerdeira","last_name":"Oliveira","full_name":"Oliveira, Afonso De Cerdeira"},{"last_name":"Chrastina","full_name":"Chrastina, Daniel","first_name":"Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"id":"1f6212b5-f795-11ec-9c0c-de4780302890","full_name":"Bubis, Anton","last_name":"Bubis","first_name":"Anton"},{"full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios"}],"article_type":"original","publication_identifier":{"issn":["0003-6951"],"eissn":["1077-3118"]},"publisher":"AIP Publishing","scopus_import":"1","supplementarymaterial":"yes","_id":"22619","date_created":"2026-08-02T22:01:53Z"},{"scopus_import":"1","file":[{"content_type":"application/pdf","date_created":"2026-08-03T12:12:03Z","date_updated":"2026-08-03T12:12:03Z","file_name":"2026_ForumMathematics_Browning.pdf","file_size":810718,"success":1,"checksum":"e92a762e03f832bdca8c106a9a88ef9b","file_id":"22636","access_level":"open_access","relation":"main_file","creator":"dernst"}],"publisher":"Cambridge University Press","publication_identifier":{"eissn":["2050-5094"]},"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","first_name":"Timothy D"},{"first_name":"Jakob","full_name":"Glas, Jakob","last_name":"Glas","id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb"},{"first_name":"Victor","orcid":"0000-0002-0704-7026","full_name":"Wang, Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","last_name":"Wang"}],"DOAJ_listed":"1","article_type":"original","quality_controlled":"1","title":"Sums of three cubes over a function field","_id":"22618","date_created":"2026-08-02T22:01:52Z","file_date_updated":"2026-08-03T12:12:03Z","supplementarymaterial":"no","language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","year":"2026","intvolume":" 14","oa":1,"volume":14,"publication":"Forum of Mathematics Sigma","day":"22","arxiv":1,"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.","PlanS_conform":"1","abstract":[{"text":"We use a function field version of the circle method to prove that a positive proportion of elements in 𝔽𝑞[𝑡] are representable as a sum of three cubes of minimal degree from 𝔽𝑞[𝑡], assuming a suitable form of the Ratios Conjecture and that char(𝔽𝑞) >3. The analogue of this conjecture for quadratic Dirichlet L-functions is known for large fixed q, via recent developments in homological stability.","lang":"eng"}],"month":"07","type":"journal_article","external_id":{"arxiv":["2402.07146"]},"das_tickbox":"0","oa_version":"Published Version","citation":{"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.","ista":"Browning TD, Glas J, Wang V. 2026. Sums of three cubes over a function field. Forum of Mathematics Sigma. 14, e112.","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","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.","short":"T.D. Browning, J. Glas, V. 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Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices. 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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."}],"month":"07","type":"research_data","oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/AT-ISTA-22242","date_updated":"2026-08-03T11:08:38Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"has_accepted_license":"1","article_processing_charge":"No"},{"date_updated":"2026-08-04T06:47:13Z","fulldoi":"https://doi.org/10.1021/jacs.6c07859","issue":"29","publication_status":"published","researchdata_availability":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"},{"_id":"LifeSc"},{"_id":"GradSch"},{"_id":"CaGo"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","pmid":1,"doi":"10.1021/jacs.6c07859","OA_type":"hybrid","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"status":"public","citation":{"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.","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.","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","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.","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.","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.","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"},"ddc":["540"],"date_published":"2026-07-15T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"type":"journal_article","external_id":{"pmid":["42532904"]},"das_tickbox":"0","oa_version":"Published Version","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."}],"month":"07","day":"15","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.","PlanS_conform":"1","publication":"Journal of the AmericanChemical Society","volume":148,"intvolume":" 148","oa":1,"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","year":"2026","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"supplementarymaterial":"yes","date_created":"2026-08-04T06:29:31Z","_id":"22645","page":"31245-31252","file_date_updated":"2026-08-04T06:40:17Z","author":[{"full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","orcid":"0000-0002-6962-8598","first_name":"Seungho"},{"last_name":"Balazs","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","first_name":"Daniel","orcid":"0000-0001-7597-043X"},{"full_name":"Rayaroth Puthiyaveettil, Aiswarya","id":"8aceb01b-8972-11ed-ae7b-d5fe53775add","last_name":"Rayaroth Puthiyaveettil","first_name":"Aiswarya"},{"full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Engel, Michael","last_name":"Engel","first_name":"Michael"},{"id":"d03b62b2-5976-11ef-a8d7-9525504b7895","last_name":"Cherniukh","full_name":"Cherniukh, Ihor","first_name":"Ihor"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843"}],"article_type":"original","quality_controlled":"1","title":"Reaction medium asan architect of nanocrystal superlattices","scopus_import":"1","file":[{"file_size":6564594,"date_created":"2026-08-04T06:40:17Z","date_updated":"2026-08-04T06:40:17Z","file_name":"2026_JACS_Lee.pdf","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"22646","checksum":"063314ae5ac4225ebd4436aa8707d113","success":1}],"publisher":"American Chemical Society","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]}},{"researchdata_availability":"upon request","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1103/71f2-sq4p","date_updated":"2026-08-04T06:07:20Z","publication_status":"published","issue":"2","article_number":"023302","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"OnHo"},{"_id":"GradSch"}],"tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2026-08-03T00:00:00Z","ddc":["530"],"citation":{"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.","short":"E.-F. Gheorghita, S. Wald, A. Pupić, O. Hosten, Physical Review A 114 (2026).","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.","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.","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","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.","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"},"project":[{"grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}],"status":"public","OA_type":"hybrid","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.","doi":"10.1103/71f2-sq4p","month":"08","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","das_tickbox":"1","external_id":{"arxiv":["2512.14528"]},"type":"journal_article","publication":"Physical Review A","volume":114,"PlanS_conform":"1","arxiv":1,"day":"03","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).","year":"2026","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","oa":1,"intvolume":" 114","date_created":"2026-08-04T05:58:23Z","_id":"22642","file_date_updated":"2026-08-04T06:03:14Z","supplementarymaterial":"yes","publisher":"American Physical Society","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"scopus_import":"1","file":[{"checksum":"fdecc394b734b56e1b3b151a816bbe14","success":1,"access_level":"open_access","file_id":"22643","creator":"dernst","relation":"main_file","date_updated":"2026-08-04T06:03:14Z","date_created":"2026-08-04T06:03:14Z","file_name":"2026_PhysicalReviewA_Gheorghita.pdf","content_type":"application/pdf","file_size":959463}],"quality_controlled":"1","title":"Continuous accumulation of cold atoms in an optical cavity","author":[{"last_name":"Gheorghita","id":"e664a051-133f-11ed-8f02-a05999ad0822","full_name":"Gheorghita, Edward-Fulbright","first_name":"Edward-Fulbright"},{"first_name":"Sebastian","orcid":"0000-0002-5869-1604","full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","last_name":"Wald"},{"first_name":"Andrea","full_name":"Pupić, Andrea","id":"ef9c50a4-5335-11ef-8b9b-8ce03e6380ed","last_name":"Pupić"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","first_name":"Onur"}],"article_type":"original"},{"day":"20","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.","publication":"New Phytologist","oa":1,"language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","year":"2026","supplementarymaterial":"yes","_id":"22647","date_created":"2026-08-04T06:48:41Z","author":[{"first_name":"Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gackowski, Adam","last_name":"Gackowski","first_name":"Adam"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","first_name":"Ivana"},{"first_name":"Saqer S.","full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"article_type":"original","quality_controlled":"1","title":"The role of clathrin in post‐Golgi secretion in plant cells","scopus_import":"1","publisher":"Wiley","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"fulldoi":"https://doi.org/10.1111/nph.71454","date_updated":"2026-08-04T07:58:27Z","publication_status":"epub_ahead","researchdata_availability":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"GradSch"}],"article_processing_charge":"Yes (via OA deal)","article_number":"nph.71454","pmid":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).","OA_type":"hybrid","doi":"10.1111/nph.71454","main_file_link":[{"url":"https://doi.org/10.1111/nph.71454","open_access":"1"}],"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"status":"public","citation":{"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.","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","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.","short":"M. Adamowski, A. Gackowski, I. Matijevic, S.S. Alotaibi, J. Friml, New Phytologist (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.","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.","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"},"date_published":"2026-07-20T00:00:00Z","type":"journal_article","external_id":{"pmid":["42477503"]},"das_tickbox":"1","oa_version":"Published Version","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."}],"month":"07"},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","arxiv":1,"day":"17","PlanS_conform":"1","volume":116,"publication":"Letters in Mathematical Physics","intvolume":" 116","oa":1,"corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"year":"2026","supplementarymaterial":"no","file_date_updated":"2026-08-04T05:55:58Z","_id":"22639","date_created":"2026-08-03T13:21:14Z","author":[{"full_name":"Desio, Davide","id":"ea10a57b-23f6-11ef-9085-80d8596d52ef","last_name":"Desio","first_name":"Davide","orcid":"0000-0001-9840-3809"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"article_type":"original","title":"Dyson expansion for form-bounded perturbations and applications to the polaron problem","quality_controlled":"1","file":[{"success":1,"checksum":"1b90ff7da16b9604d6fe2c6281493456","relation":"main_file","creator":"dernst","file_id":"22641","access_level":"open_access","file_size":371840,"content_type":"application/pdf","file_name":"2026_LettersMathPhysics_Desio.pdf","date_updated":"2026-08-04T05:55:58Z","date_created":"2026-08-04T05:55:58Z"}],"scopus_import":"1","publication_identifier":{"issn":["1573-0530"]},"publisher":"Springer Nature","issue":"4","publication_status":"published","fulldoi":"https://doi.org/10.1007/s11005-026-02107-2","date_updated":"2026-08-04T05:57:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","researchdata_availability":"no","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_number":"87","OA_type":"hybrid","doi":"10.1007/s11005-026-02107-2","status":"public","ddc":["510"],"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","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.","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.","short":"D. Desio, R. Seiringer, Letters in Mathematical Physics 116 (2026).","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.","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.","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"},"date_published":"2026-07-17T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"type":"journal_article","external_id":{"arxiv":["2512.13443"]},"oa_version":"Published Version","das_tickbox":"0","abstract":[{"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.","lang":"eng"}],"month":"07"},{"researchdata_availability":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1017/s0017089526101074","date_updated":"2026-08-04T06:28:01Z","publication_status":"epub_ahead","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"TiBr"},{"_id":"GradSch"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0017089526101074"}],"status":"public","doi":"10.1017/s0017089526101074","OA_type":"hybrid","date_published":"2026-07-21T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"ddc":["500"],"citation":{"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.","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","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","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.","ista":"Diao Y. 2026. Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal., 1–34.","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.","short":"Y. Diao, Glasgow Mathematical Journal (2026) 1–34."},"das_tickbox":"0","oa_version":"Published Version","external_id":{"arxiv":["2506.18065"]},"type":"journal_article","month":"07","abstract":[{"lang":"eng","text":"We analyze the average behavior of various arithmetic functions at the values of degree 𝑑 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 𝑒 and by varying binary forms of fixed degree 𝑑, provided 𝑒 divides 𝑑. This proves an average version of a conjecture of Colliot-Thélène."}],"PlanS_conform":"1","day":"21","arxiv":1,"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.","publication":"Glasgow Mathematical Journal","oa":1,"year":"2026","mathsc":["11N32","11N37","11D57","11G35"],"language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","supplementarymaterial":"no","_id":"22644","page":"1-34","date_created":"2026-08-04T06:15:04Z","quality_controlled":"1","title":"Liouville function, von Mangoldt function, and norm forms at random binary forms","author":[{"full_name":"Diao, Yijie","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","last_name":"Diao","orcid":"0000-0002-4989-5330","first_name":"Yijie"}],"article_type":"original","publisher":"Cambridge University Press","publication_identifier":{"eissn":["1469-509X"],"issn":["0017-0895"]},"scopus_import":"1"},{"supplementarymaterial":"yes","_id":"21923","date_created":"2026-05-29T13:25:16Z","file_date_updated":"2026-05-29T13:19:37Z","quality_controlled":"1","title":"Physics-inspired procedural texturing of extremely deformable surfaces","author":[{"first_name":"Aleksei","orcid":"0000-0003-2189-3904","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","full_name":"Kalinov, Aleksei"},{"last_name":"Ly","full_name":"Ly, Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"Mickaël"},{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J"}],"article_type":"original","publisher":"Association for Computing Machinery","publication_identifier":{"issn":["0730-0301"]},"scopus_import":"1","file":[{"file_size":77337231,"date_created":"2026-05-29T13:19:33Z","date_updated":"2026-05-29T13:19:33Z","file_name":"tog454-article154-supplemental.mp4","content_type":"video/mp4","relation":"main_file","creator":"akalinov","access_level":"open_access","file_id":"21924","checksum":"ea165bf731ddd3045f83878dcb833672","success":1},{"file_size":226633977,"content_type":"video/mp4","file_name":"tog454-article154-video.mp4","date_created":"2026-05-29T13:19:37Z","date_updated":"2026-05-29T13:19:37Z","relation":"main_file","creator":"akalinov","file_id":"21925","access_level":"open_access","success":1,"checksum":"6274cfb15ea5ba7324b74afc7b0d9629"},{"success":1,"checksum":"9d41b322a7876be9a3311017b9973183","file_id":"21926","access_level":"open_access","relation":"main_file","creator":"akalinov","content_type":"application/pdf","date_updated":"2026-05-29T13:19:33Z","date_created":"2026-05-29T13:19:33Z","file_name":"tog454-article154-supplemental.pdf","file_size":6793867},{"checksum":"51bc60d2de867fbfa570652dec7993b4","success":1,"access_level":"open_access","file_id":"21927","creator":"akalinov","relation":"main_file","date_updated":"2026-05-29T13:19:36Z","date_created":"2026-05-29T13:19:36Z","file_name":"tog454-article154-main-1.pdf","content_type":"application/pdf","file_size":84173392}],"day":"01","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).","publication":"ACM Transactions on Graphics","volume":45,"oa":1,"conference":{"name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","location":"Los Angeles, CA, United States","start_date":"2026-07-19","end_date":"2026-07-23"},"intvolume":" 45","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2026","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"status":"public","OA_type":"gold","doi":"10.1145/3811353","date_published":"2026-07-01T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"citation":{"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.","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.","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","short":"A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45 (2026).","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.","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","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."},"ddc":["006"],"oa_version":"Published Version","das_tickbox":"0","type":"journal_article","month":"07","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."}],"related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/infinite-deformation-and-shape-computation/"}]},"keyword":["Procedural animation"],"researchdata_availability":"no","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-08-04T09:07:44Z","fulldoi":"https://doi.org/10.1145/3811353","issue":"4","publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"article_number":"154"},{"researchdata_availability":"yes","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","fulldoi":"https://doi.org/10.1038/s41586-026-10679-1","date_updated":"2026-08-04T09:29:55Z","publication_status":"epub_ahead","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"AnKi"},{"_id":"GaNo"},{"_id":"TiVo"},{"_id":"ScienComp"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41586-026-10679-1","open_access":"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"},{"grant_number":"FG1803 49015","name":"Neurobiology of anxiety in autism spectrum disorders","_id":"ebb38b5d-77a9-11ec-83b8-a42e08120a88"}],"status":"public","OA_type":"hybrid","doi":"10.1038/s41586-026-10679-1","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).","tmp":{"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)","image":"/images/cc_by.png"},"date_published":"2026-06-17T00:00:00Z","citation":{"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","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.","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","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.","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.","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).","ieee":"L. A. Schwarz et al., “Cortical development dynamics across autism spectrum disorder mouse models,” Nature. Springer Nature, 2026."},"ddc":["570"],"oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["42310454"]},"month":"06","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/patterns-in-genetic-chaos/"}]},"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."}],"PlanS_conform":"1","day":"17","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).","publication":"Nature","oa":1,"year":"2026","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","supplementarymaterial":"yes","date_created":"2026-07-13T09:47:21Z","_id":"22295","quality_controlled":"1","title":"Cortical development dynamics across autism spectrum disorder mouse models","article_type":"original","author":[{"first_name":"Lena A","full_name":"Schwarz, Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","first_name":"Christoph"},{"full_name":"Isaev, Sergey","last_name":"Isaev","first_name":"Sergey"},{"first_name":"Michela","id":"39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c","last_name":"Lisi","full_name":"Lisi, Michela"},{"first_name":"Daniel","full_name":"Malzl, Daniel","last_name":"Malzl"},{"first_name":"Christoph","full_name":"Büschl, Christoph","last_name":"Büschl","id":"2a8c054c-0913-11ee-9159-f8ef515809ed"},{"full_name":"Ladstätter, Sabrina","last_name":"Ladstätter","first_name":"Sabrina"},{"first_name":"Bárbara","last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara"},{"last_name":"Barel","id":"8959927b-2236-11ed-bd6e-ea83d94ade0e","full_name":"Barel, Matteo","first_name":"Matteo"},{"first_name":"Bernadette","orcid":"0000-0003-1843-3173","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","last_name":"Basilico","full_name":"Basilico, Bernadette"},{"last_name":"Chintaluri","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","full_name":"Chintaluri, Chaitanya","orcid":"0000-0003-4252-1608","first_name":"Chaitanya"},{"id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","last_name":"Gorkiewicz","full_name":"Gorkiewicz, Sarah","first_name":"Sarah"},{"last_name":"Goudarzi","full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","first_name":"Mohammad"},{"last_name":"Belinova","full_name":"Belinova, Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","first_name":"Tereza"},{"first_name":"Stephan","full_name":"Reichl, Stephan","last_name":"Reichl"},{"first_name":"Gintarė","id":"dd6d52f2-c50d-11eb-9548-bcf0ff82b344","full_name":"Sendžikaitė, Gintarė","last_name":"Sendžikaitė"},{"full_name":"Arcot Jayaram, Satish","last_name":"Arcot Jayaram","id":"b0bbee33-09f7-11eb-909c-8b358058d28a","orcid":"0000-0002-2479-2669","first_name":"Satish"},{"first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","first_name":"Tim P","orcid":"0000-0003-3295-6181"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"first_name":"Igor","last_name":"Adameyko","full_name":"Adameyko, Igor"},{"first_name":"Peter Vasili","last_name":"Kharchenko","id":"0095641e-7eb7-11f1-8665-aec51a2ab5e0","full_name":"Kharchenko, Peter Vasili"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"scopus_import":"1"},{"pmid":1,"department":[{"_id":"PaSc"},{"_id":"AlBr"},{"_id":"GradSch"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"epub_ahead","fulldoi":"https://doi.org/10.1038/s41587-026-03166-5","date_updated":"2026-08-04T09:25:18Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","researchdata_availability":"yes","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."}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/toward-experiment-guided-alphafold/","description":"News on ISTA website"}]},"month":"06","type":"journal_article","external_id":{"pmid":["42374114"]},"das_tickbox":"1","oa_version":"Published Version","ddc":["570"],"citation":{"ieee":"S. A. Maddipatla et al., “Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles,” Nature Biotechnology. Springer Nature, 2026.","short":"S.A. Maddipatla, N.E. Sellam, M.I. Bojan, V. Masalitin, S. Vedula, P. Schanda, A. Marx, A.M. Bronstein, Nature Biotechnology (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.","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.","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","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.","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"},"date_published":"2026-06-29T00:00:00Z","tmp":{"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)","image":"/images/cc_by.png"},"OA_type":"hybrid","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","doi":"10.1038/s41587-026-03166-5","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-026-03166-5"}],"OA_place":"publisher","corr_author":"1","language":[{"iso":"eng"}],"year":"2026","oa":1,"publication":"Nature Biotechnology","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).","day":"29","PlanS_conform":"1","scopus_import":"1","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"publisher":"Springer Nature","author":[{"full_name":"Maddipatla, Sai A","id":"e957f5e5-91c9-11f0-a95f-e090f66ecb4d","last_name":"Maddipatla","first_name":"Sai A"},{"last_name":"Sellam","full_name":"Sellam, Nadav E","id":"ef280fe0-91c9-11f0-a95f-8dea3f5bc513","first_name":"Nadav E"},{"first_name":"Meital I","full_name":"Bojan, Meital I","id":"11d88cf5-91ca-11f0-a95f-edf9f08f47b7","last_name":"Bojan"},{"first_name":"Vova","last_name":"Masalitin","full_name":"Masalitin, Vova","id":"ff7958eb-91c9-11f0-a95f-f3bf65828cf6"},{"first_name":"Sanketh","last_name":"Vedula","full_name":"Vedula, Sanketh"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"last_name":"Marx","full_name":"Marx, Ailie","first_name":"Ailie"},{"id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","last_name":"Bronstein","full_name":"Bronstein, Alexander","first_name":"Alexander","orcid":"0000-0001-9699-8730"}],"article_type":"original","title":"Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles","quality_controlled":"1","_id":"22268","date_created":"2026-07-12T22:02:19Z","supplementarymaterial":"yes"},{"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"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12675"},{"relation":"part_of_dissertation","id":"21777","status":"public"},{"relation":"part_of_dissertation","id":"12114","status":"public"},{"status":"public","id":"22105","relation":"part_of_dissertation"}]},"month":"07","type":"dissertation","das_tickbox":"1","oa_version":"Published Version","ddc":["572"],"citation":{"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","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.","ieee":"L. M. Becker, “Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026.","short":"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.","ama":"Becker LM. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. 2026. doi: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."},"date_published":"2026-07-13T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.15479/AT-ISTA-22334","project":[{"name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"status":"public","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"has_accepted_license":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.15479/AT-ISTA-22334","date_updated":"2026-08-04T09:32:45Z","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"access_level":"closed","file_id":"22346","creator":"lbecker","relation":"source_file","checksum":"8b85114eff543916c0e1445cd2189555","file_name":"2026_Becker_Lea_source_files.zip","date_updated":"2026-07-16T09:17:08Z","date_created":"2026-07-16T09:17:08Z","content_type":"application/zip","file_size":99472908},{"file_size":74647289,"file_name":"2026_Becker_Lea_Thesis.pdf","date_created":"2026-07-16T09:17:05Z","date_updated":"2026-07-16T09:17:05Z","content_type":"application/pdf","checksum":"6c526862bc6dbd1e4c80ecb34580bc58","success":1,"creator":"lbecker","relation":"main_file","access_level":"open_access","file_id":"22347"}],"doi_confirm":"1","publisher":"Institute of Science and Technology Austria","publication_identifier":{"isbn":["978-3-99078-084-8"],"issn":["2663-337X"]},"author":[{"last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie","first_name":"Lea Marie","orcid":"0000-0002-6401-5151"}],"title":"Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR","_id":"22334","date_created":"2026-07-14T08:08:51Z","page":"205","file_date_updated":"2026-07-16T09:17:08Z","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","year":"2026","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"NMR"}],"oa":1,"supervisor":[{"first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"day":"13","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).","degree_awarded":"PhD"}]