--- OA_place: repository _id: '21393' abstract: - lang: eng text: "This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X citation: ama: 'Dvorak M. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. 2026. doi:10.15479/AT-ISTA-21393' apa: 'Dvorak, M. (2026). Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21393' chicago: 'Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21393.' ieee: 'M. Dvorak, “Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026.' ista: 'Dvorak M. 2026. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria.' mla: 'Dvorak, Martin. Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21393.' short: 'M. Dvorak, Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-03-04T09:26:46Z date_published: 2026-03-04T00:00:00Z date_updated: 2026-03-27T12:37:00Z day: '04' ddc: - '511' - '000' degree_awarded: PhD department: - _id: GradSch - _id: VlKo doi: 10.15479/AT-ISTA-21393 file: - access_level: open_access checksum: cface6dc18152680962b5361575f6e4f content_type: application/pdf creator: mdvorak date_created: 2026-03-04T08:56:15Z date_updated: 2026-03-04T08:56:15Z file_id: '21394' file_name: 2026_Dvorak_Martin_Thesis.pdf file_size: 1771231 relation: main_file success: 1 - access_level: closed checksum: 290ddfacfb7e07fb07e6f0b334e67c90 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mdvorak date_created: 2026-03-04T09:03:37Z date_updated: 2026-03-04T09:03:37Z file_id: '21395' file_name: 2026_Dvorak_Martin_Thesis.docx file_size: 864585 relation: source_file file_date_updated: 2026-03-04T09:03:37Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '160' publication_identifier: isbn: - 978-3-99078-074-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: link: - description: Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality) relation: software url: https://github.com/madvorak/duality/tree/v3.5.0 - description: Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems) relation: software url: https://github.com/madvorak/vcsp/tree/v8.2.0 - description: Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project) relation: software url: https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0 - description: Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars) relation: software url: https://github.com/madvorak/chomsky/tree/v1.2.0 - description: Old version (Lean 3) of the project about grammars relation: software url: https://github.com/madvorak/grammars - description: Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis relation: software url: https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean record: - id: '13120' relation: part_of_dissertation status: public - id: '21398' relation: part_of_dissertation status: public - id: '20071' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Jasmin full_name: Blanchette, Jasmin last_name: Blanchette title: 'Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21501' abstract: - lang: eng text: "Kinetically constrained models were originally introduced to capture slow relaxation in glassy systems, where dynamics are hindered by local constraints instead of energy barriers. Their quantum counterparts have recently drawn attention for exhibiting highly degenerate eigenstates at zero energy—known as zero modes—stemming from chiral symmetry. Yet, the structure and implications of these zero modes remain poorly understood. In this work, we focus on the properties of the zero mode subspace in quantum kinetically constrained models with a U(1) particle-conservation symmetry. We use the U(1) East, which lacks inversion symmetry, and the inversion-symmetric U(1) East-West models to illustrate our two main results. First, we observe that the simultaneous presence of constraints and chiral symmetry generally leads to a parametric increase in the number of zero modes due to the fragmentation of the many-body\r\nHilbert space into disconnected sectors. Second, we generalize the concept of compact localized states from single-particle physics and introduce the notion of collective bound states, a special kind of nonergodic eigenstates that are robust to enlarging the system size. We formulate sufficient criteria for their existence, arguing that the degenerate zero mode subspace plays a central role, and demonstrate bound states in both example models and in a two-dimensional model, the U(1) North-East, and in the pairflip model, a system without particle conservation. Our results motivate a systematic study of bound states and their relation to ergodicity breaking, transport, and other properties of quantum kinetically constrained\r\nmodels. " acknowledgement: The authors acknowledge useful discussions with Berislav Buca. This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. This research was supported in part by grant NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP). article_number: '010352' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Eulalia full_name: Nicolau Jimenez, Eulalia id: 04b4791c-8fd7-11ee-a7df-be2fdc569c48 last_name: Nicolau Jimenez - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Nicolau Jimenez E, Ljubotina M, Serbyn M. Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. 2026;7. doi:10.1103/sl79-1xgb apa: Nicolau Jimenez, E., Ljubotina, M., & Serbyn, M. (2026). Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. American Physical Society. https://doi.org/10.1103/sl79-1xgb chicago: Nicolau Jimenez, Eulalia, Marko Ljubotina, and Maksym Serbyn. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” PRX Quantum. American Physical Society, 2026. https://doi.org/10.1103/sl79-1xgb. ieee: E. Nicolau Jimenez, M. Ljubotina, and M. Serbyn, “Fragmentation, zero modes, and collective bound states in constrained models,” PRX Quantum, vol. 7. American Physical Society, 2026. ista: Nicolau Jimenez E, Ljubotina M, Serbyn M. 2026. Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. 7, 010352. mla: Nicolau Jimenez, Eulalia, et al. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” PRX Quantum, vol. 7, 010352, American Physical Society, 2026, doi:10.1103/sl79-1xgb. short: E. Nicolau Jimenez, M. Ljubotina, M. Serbyn, PRX Quantum 7 (2026). corr_author: '1' date_created: 2026-03-28T14:57:56Z date_published: 2026-03-13T00:00:00Z date_updated: 2026-03-30T06:09:28Z day: '13' ddc: - '530' department: - _id: MaSe doi: 10.1103/sl79-1xgb ec_funded: 1 external_id: arxiv: - '2504.17627' file: - access_level: open_access checksum: d155ffa9e1a8275702149165f4bf963c content_type: application/pdf creator: dernst date_created: 2026-03-30T06:08:07Z date_updated: 2026-03-30T06:08:07Z file_id: '21505' file_name: 2026_PRXQuantum_Nicolau.pdf file_size: 1848724 relation: main_file success: 1 file_date_updated: 2026-03-30T06:08:07Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: PRX Quantum publication_identifier: eissn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Fragmentation, zero modes, and collective bound states in constrained models tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21483' abstract: - lang: eng text: 'Embryogenesis in the model plant Arabidopsis thaliana provides a framework for understanding how cell polarity and patterning coordinate with hormonal signalling to establish the plant body plan. Following fertilisation, the zygote divides asymmetrically to generate apical and basal lineages, establishing the apical–basal axis that defines future shoot and root poles. Genetic and molecular analyses of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless revealed that localised auxin biosynthesis, directional transport and downstream transcriptional responses are central to apical–basal axis establishment and organ initiation. The main components of this regulation are polarly localised PIN auxin transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX transcription factors. Advances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning and multiphoton microscopes enable real-time observation of embryo development, while laser-assisted cell ablation can be used to probe cell-to-cell communication and fate plasticity. Together, these methodological breakthroughs position Arabidopsis embryos as a prime model for dissecting the chemical and biophysical cues that shape plant development.' acknowledgement: The authors would like to acknowledge the many colleagues whose valuable contributions to the field could not be included in this review due to space limitations and reference constraints. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ. article_number: nph.71072 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic - first_name: Milan full_name: Zupunski, Milan id: f6a21fce-573e-11f0-a150-a8d96aee2539 last_name: Zupunski - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Babic D, Zupunski M, Friml J. Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist. 2026. doi:10.1111/nph.71072 apa: Babic, D., Zupunski, M., & Friml, J. (2026). Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist. Wiley. https://doi.org/10.1111/nph.71072 chicago: Babic, David, Milan Zupunski, and Jiří Friml. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71072. ieee: D. Babic, M. Zupunski, and J. Friml, “Imaging and genetic toolbox to study Arabidopsis embryogenesis,” New Phytologist. Wiley, 2026. ista: Babic D, Zupunski M, Friml J. 2026. Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist., nph. 71072. mla: Babic, David, et al. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” New Phytologist, nph. 71072, Wiley, 2026, doi:10.1111/nph.71072. short: D. Babic, M. Zupunski, J. Friml, New Phytologist (2026). corr_author: '1' date_created: 2026-03-23T14:59:06Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-03-30T05:58:35Z day: '11' department: - _id: JiFr - _id: GradSch doi: 10.1111/nph.71072 external_id: pmid: - '41808651' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nph.71072 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: epub_ahead publisher: Wiley quality_controlled: '1' status: public title: Imaging and genetic toolbox to study Arabidopsis embryogenesis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21502' abstract: - lang: eng text: The mammalian brain stores glucose, the main circulating energy substrate, as glycogen. In rodents, the cerebellum contains relatively high glycogen levels, yet its cellular and subcellular distribution remains poorly defined. Using monoclonal antibodies against glycogen, we examined its distribution in the mouse cerebellar cortex. Glycogen was predominantly localized to Bergmann glia (BG) processes in the molecular layer and was also detected in Purkinje cells (PCs), the principal cerebellar neurons. To assess the functional significance of cerebellar glycogen, we analyzed behavior in mice lacking glycogen synthase 1 (Gys1) in BG or PCs using a floxed Gys1 line. Gys1 deficiency in either PCs or GFAP-positive cells reduced anxiety-like behavior, whereas combined deletion caused PC degeneration and ataxia. These findings reveal a critical role for glycogen metabolism in both astrocytes and neurons in cerebellar function. acknowledgement: This work was supported by the Novo Nordisk Foundation (NNFOC0058058, H. Hirase), the Danmarks Frie Forskningsfond (0134-00107B and 5283-00069A, H.Hirase), the Lundbeck Foundation, Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) program (22K06454/24H01221, A.K.; 23K27482, H.Hirai), the Japan Agency for Medical Research and Development (AMED) Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS) (JP21dm0207111, H. Hirai), AMED Brain/MINDS 2.0 (JP23wm0625001 and JP24wm0625103, H. Hirai), and grants from the Spanish Ministerio de Ciencia e Innovación (MCIU/FEDER/AEI) (PID2020-118699 GB-100, J.D.) and the Fundación Ramón Areces (J.D.). Sonam Akther has been supported by the RIKEN IPA fellowship. We are thankful to Dr. Yuki Oe for his support in the initial stage of this study and to Dan Xue for his help with the graphical abstract. We thank Dr. Pia Weikop for providing CTN research infrastructure. The authors declare no competing financial interests. article_number: '115192' article_processing_charge: Yes article_type: original author: - first_name: Sonam full_name: Akther, Sonam last_name: Akther - first_name: Ashley Bomin full_name: Lee, Ashley Bomin last_name: Lee - first_name: Ayumu full_name: Konno, Ayumu last_name: Konno - first_name: Antonis full_name: Asiminas, Antonis last_name: Asiminas - first_name: Marta full_name: Vittani, Marta last_name: Vittani - first_name: Tsuneko full_name: Mishima, Tsuneko last_name: Mishima - first_name: Hirokazu full_name: Hirai, Hirokazu last_name: Hirai - first_name: Claire Francesca full_name: Meehan, Claire Francesca last_name: Meehan - first_name: Jordi full_name: Duran, Jordi last_name: Duran - first_name: Joan full_name: Guinovart, Joan last_name: Guinovart - first_name: Hitoshi full_name: Ashida, Hitoshi last_name: Ashida - first_name: Tsuyoshi full_name: Morita, Tsuyoshi last_name: Morita - first_name: Otto full_name: Baba, Otto last_name: Baba - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Maiken full_name: Nedergaard, Maiken last_name: Nedergaard - first_name: Hajime full_name: Hirase, Hajime last_name: Hirase citation: ama: Akther S, Lee AB, Konno A, et al. Distribution and functional significance of rodent cerebellar glycogen. iScience. 2026;29(4). doi:10.1016/j.isci.2026.115192 apa: Akther, S., Lee, A. B., Konno, A., Asiminas, A., Vittani, M., Mishima, T., … Hirase, H. (2026). Distribution and functional significance of rodent cerebellar glycogen. IScience. Elsevier. https://doi.org/10.1016/j.isci.2026.115192 chicago: Akther, Sonam, Ashley Bomin Lee, Ayumu Konno, Antonis Asiminas, Marta Vittani, Tsuneko Mishima, Hirokazu Hirai, et al. “Distribution and Functional Significance of Rodent Cerebellar Glycogen.” IScience. Elsevier, 2026. https://doi.org/10.1016/j.isci.2026.115192. ieee: S. Akther et al., “Distribution and functional significance of rodent cerebellar glycogen,” iScience, vol. 29, no. 4. Elsevier, 2026. ista: Akther S, Lee AB, Konno A, Asiminas A, Vittani M, Mishima T, Hirai H, Meehan CF, Duran J, Guinovart J, Ashida H, Morita T, Baba O, Shigemoto R, Nedergaard M, Hirase H. 2026. Distribution and functional significance of rodent cerebellar glycogen. iScience. 29(4), 115192. mla: Akther, Sonam, et al. “Distribution and Functional Significance of Rodent Cerebellar Glycogen.” IScience, vol. 29, no. 4, 115192, Elsevier, 2026, doi:10.1016/j.isci.2026.115192. short: S. Akther, A.B. Lee, A. Konno, A. Asiminas, M. Vittani, T. Mishima, H. Hirai, C.F. Meehan, J. Duran, J. Guinovart, H. Ashida, T. Morita, O. Baba, R. Shigemoto, M. Nedergaard, H. Hirase, IScience 29 (2026). date_created: 2026-03-29T22:07:07Z date_published: 2026-03-17T00:00:00Z date_updated: 2026-03-30T06:20:06Z day: '17' department: - _id: RySh doi: 10.1016/j.isci.2026.115192 external_id: pmid: - '41890976' intvolume: ' 29' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.isci.2026.115192 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: iScience publication_identifier: eissn: - 2589-0042 publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Distribution and functional significance of rodent cerebellar glycogen type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2026' ... --- OA_place: publisher _id: '20964' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Master’s Thesis article_processing_charge: No author: - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev citation: ama: Vladimirtsev D. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. 2026. doi:10.15479/AT-ISTA-20964 apa: Vladimirtsev, D. (2026). Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20964 chicago: Vladimirtsev, Dmitrii. “Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20964. ieee: D. Vladimirtsev, “Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels,” Institute of Science and Technology Austria, 2026. ista: Vladimirtsev D. 2026. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria. mla: Vladimirtsev, Dmitrii. Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20964. short: D. Vladimirtsev, Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-01-09T09:22:48Z date_published: 2026-01-14T00:00:00Z date_updated: 2026-04-07T11:41:44Z day: '14' ddc: - '570' degree_awarded: MS department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-20964 file: - access_level: closed checksum: 812857b2fbe3f6113bef22fd04bccd3e content_type: application/pdf creator: dvladimi date_created: 2026-01-21T14:12:13Z date_updated: 2026-01-21T14:12:13Z embargo: 2027-01-01 embargo_to: open_access file_id: '21033' file_name: 2026_Vladimirtsev_Dmitrii_Thesis.pdf file_size: 2867531 relation: main_file - access_level: closed checksum: 2b969f97f8d7461bea3d255f48c2219c content_type: application/x-zip-compressed creator: dvladimi date_created: 2026-01-21T14:41:58Z date_updated: 2026-01-28T12:38:19Z file_id: '21034' file_name: Source Files.zip file_size: 25023066 relation: source_file file_date_updated: 2026-01-28T12:38:19Z has_accepted_license: '1' language: - iso: eng month: '01' oa_version: Published Version page: '22' project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20982' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: publisher _id: '21198' abstract: - lang: eng text: "In recent years there has been a massive increase in the amount of data generated in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones, have become\r\nubiquitous in most societies on earth. Through text typed, photos taken and apps used,\r\nthese devices, which we refer to as clients, generate enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of these devices means the data they generate is often\r\nsensitive and privacy concerns prevent it being gathered and stored in a central location. This\r\npresents a challenge to the modern machine learning paradigm that requires central access\r\nto large amounts of data. Federated learning (FL) has emerged as one of the answers to\r\nthis problem. Rather than bringing the data to the model, FL sends the model to the data.\r\nModel training takes place on device, with periodically synchronized updates, allowing data to\r\nremain locally stored. While this approach offers significant privacy advantages it comes with\r\nits own set of unique challenges. These include: data heterogeneity, the notion that different\r\ndevices generate data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity, meaning that different devices may have differing hardware specifications; high\r\ncommunication costs, which are induced by the repeated transferring of models over the\r\nnetwork and low device computational power, which limits the use of larger models on device.\r\nIn this thesis we present a range of methods for federated learning. We focus primarily on\r\nthe challenge of data heterogeneity, though the methods presented are designed to be well\r\nadapted to the other challenges of a federated setting, such as the constraints of limited\r\ncompute and communication overhead. We first present a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates clients as samples from a certain probability\r\ndistribution and infers the parameters of this distribution from the available training clients.\r\nThis learned distribution then represents the heterogeneity present among the clients and can\r\nbe sampled from in order to create new simulated clients that are similar to the real clients we\r\nhave observed so far. Following this we present two methods for directly dealing with data\r\nheterogeneity through personalization. Highly heterogeneous client data distributions can mean\r\nthat learning a single global model becomes suboptimal, and some form of personalization of\r\nmodels to each individual client is required. Our approaches are based around hypernetworks,\r\nwhich we use to generate personalized model parameters without the need for additional\r\ntraining or finetuning. In the first approach we focus on generating full parameterizations of\r\nclient models using learned embeddings of client data and labels, with a hypernetwork located\r\non the central server. In the second approach we address the more challenging scenario where\r\nwe want to generate a personalized model for a client without any label information. The\r\nhypernetwork is trained to generate a low dimensional representation of a client’s personalized\r\nmodel parameters, allowing it to be transferred to and run on the client devices. In our final\r\npresented method, we change our focus and rather than aim to directly address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected by it. This is done in the context\r\nof k-means clustering and we present a method for federated clustering with a focus on added\r\nprivacy guarantees." acknowledged_ssus: - _id: ScienComp acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12]. Furthermore, the candidate acknowledges the support from the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott citation: ama: Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:10.15479/AT-ISTA-21198 apa: Scott, J. A. (2026). Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21198 chicago: Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated Learning.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21198. ieee: J. A. Scott, “Data heterogeneity and personalization in federated learning,” Institute of Science and Technology Austria, 2026. ista: Scott JA. 2026. Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. mla: Scott, Jonathan A. Data Heterogeneity and Personalization in Federated Learning. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21198. short: J.A. Scott, Data Heterogeneity and Personalization in Federated Learning, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-02-09T14:59:53Z date_published: 2026-02-09T00:00:00Z date_updated: 2026-04-07T11:46:11Z day: '09' ddc: - '005' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/AT-ISTA-21198 file: - access_level: closed checksum: 121c1d968bd86f3630aa7e81d5bbbcb0 content_type: application/zip creator: jscott date_created: 2026-02-17T11:46:22Z date_updated: 2026-02-17T11:46:22Z file_id: '21298' file_name: 2026_Scott_Jonathan_Thesis_Source.zip file_size: 272379252 relation: source_file - access_level: open_access checksum: 6e3e08ba474bbee8511cc8a839ab2077 content_type: application/pdf creator: jscott date_created: 2026-02-27T10:25:41Z date_updated: 2026-02-27T10:25:41Z file_id: '21366' file_name: 2026_Jonathan_Scott_Thesis.pdf file_size: 15220298 relation: main_file success: 1 file_date_updated: 2026-02-27T10:25:41Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '158' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20819' relation: part_of_dissertation status: public - id: '17411' relation: part_of_dissertation status: public - id: '18120' relation: part_of_dissertation status: public - id: '21207' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Data heterogeneity and personalization in federated learning type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: publisher _id: '21021' abstract: - lang: eng text: This thesis examines how geometry and topology intersect in the representation, transformation, and analysis of complex shapes. It considers how continuous manifolds relate to their discrete analogues, how topological structures evolve in persistence vineyards, and how tools from topological data analysis can illuminate problems in mathematical physics. Central to this exploration is the question of how structure, both geometric and topological, persists or changes under approximation, sampling, or deformation. The work develops new approaches to skeletal and grid-based representations of surfaces, reveals the full expressive capacity of persistence vineyards, and applies topological methods to the longstanding problem of equilibria in electrostatic fields. These threads braid together into a broader understanding of how topology and geometry inform one another across theory, computation, and application. acknowledged_ssus: - _id: M-Shop - _id: ScienComp acknowledgement: "The research presented in this thesis was funded by the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christopher D full_name: Fillmore, Christopher D id: 35638A5C-AAC7-11E9-B0BF-5503E6697425 last_name: Fillmore citation: ama: Fillmore CD. Braiding geometry and topology to study shapes and data. 2026. doi:10.15479/AT-ISTA-21021 apa: Fillmore, C. D. (2026). Braiding geometry and topology to study shapes and data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21021 chicago: Fillmore, Christopher D. “Braiding Geometry and Topology to Study Shapes and Data.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21021. ieee: C. D. Fillmore, “Braiding geometry and topology to study shapes and data,” Institute of Science and Technology Austria, 2026. ista: Fillmore CD. 2026. Braiding geometry and topology to study shapes and data. Institute of Science and Technology Austria. mla: Fillmore, Christopher D. Braiding Geometry and Topology to Study Shapes and Data. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21021. short: C.D. Fillmore, Braiding Geometry and Topology to Study Shapes and Data, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-01-20T21:38:40Z date_published: 2026-01-21T00:00:00Z date_updated: 2026-04-07T11:42:49Z day: '21' ddc: - '514' - '516' degree_awarded: PhD department: - _id: GradSch - _id: HeEd - _id: UlWa doi: 10.15479/AT-ISTA-21021 file: - access_level: open_access checksum: 4c0889130095c31d4e5088c5b8dfd607 content_type: application/pdf creator: cfillmor date_created: 2026-01-26T19:44:46Z date_updated: 2026-01-30T11:40:09Z file_id: '21046' file_name: 2025_Fillmore_Christopher_Thesis.pdf file_size: 55954297 relation: main_file - access_level: closed checksum: d69afb71d82ab98f856886126ee7303a content_type: application/x-zip-compressed creator: cfillmor date_created: 2026-01-26T19:46:20Z date_updated: 2026-01-26T19:46:20Z file_id: '21047' file_name: Thesis.zip file_size: 166080788 relation: source_file file_date_updated: 2026-01-30T11:40:09Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '122' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20260' relation: part_of_dissertation status: public - id: '21050' relation: part_of_dissertation status: public - id: '21051' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: Braiding geometry and topology to study shapes and data tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_place: repository _id: '21051' abstract: - lang: eng text: 'In this work, we introduce and study what we believe is an intriguing and, to the best of our knowledge, previously unknown connection between two areas in computational topology, topological data analysis (TDA) and knot theory. Given a function from a topological space to $\mathbb{R}$, TDA provides tools to simplify and study the importance of topological features: in particular, the $l^{th}$-dimensional persistence diagram encodes the $l$-homology in the sublevel set as the function value increases as a set of points in the plane. Given a continuous one-parameter family of such functions, we can combine the persistence diagrams into an object known as a vineyard, which track the evolution of points in the persistence diagram. If we further restrict that family of functions to be periodic, we identify the two ends of the vineyard, yielding a closed vineyard. This allows the study of monodromy, which in this context means that following the family of functions for a period permutes the set of points in a non-trivial way. In this work, given a link and value $l$, we construct a topological space and periodic family of functions such that the closed $l$-vineyard contains this link. This shows that vineyards are topologically as rich as one could possibly hope. Importantly, it has at least two immediate consequences: First, monodromy of any periodicity can occur in a $l$-vineyard, answering a variant of a question by [Arya et al 2024]. To exhibit this, we also reformulate monodromy in a more geometric way, which may be of interest in itself. Second, distinguishing vineyards is likely to be difficult given the known difficulty of knot and link recognition, which have strong connections to many NP-hard problems.' article_processing_charge: No arxiv: 1 author: - first_name: Erin full_name: ' Chambers, Erin' last_name: ' Chambers' - first_name: Christopher D full_name: Fillmore, Christopher D id: 35638A5C-AAC7-11E9-B0BF-5503E6697425 last_name: Fillmore - first_name: Elizabeth R full_name: Stephenson, Elizabeth R id: 2D04F932-F248-11E8-B48F-1D18A9856A87 last_name: Stephenson orcid: 0000-0002-6862-208X - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. Braiding vineyards. arXiv. doi:10.48550/ARXIV.2504.11203 apa: Chambers, E., Fillmore, C. D., Stephenson, E. R., & Wintraecken, M. (n.d.). Braiding vineyards. arXiv. https://doi.org/10.48550/ARXIV.2504.11203 chicago: Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “Braiding Vineyards.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2504.11203. ieee: E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “Braiding vineyards,” arXiv. . ista: Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. Braiding vineyards. arXiv, 10.48550/ARXIV.2504.11203. mla: Chambers, Erin, et al. “Braiding Vineyards.” ArXiv, doi:10.48550/ARXIV.2504.11203. short: E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, ArXiv (n.d.). corr_author: '1' date_created: 2026-01-27T14:41:44Z date_published: 2026-01-02T00:00:00Z date_updated: 2026-04-07T11:42:48Z day: '02' department: - _id: HeEd doi: 10.48550/ARXIV.2504.11203 external_id: arxiv: - '2504.11203' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2504.11203 month: '01' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '21056' relation: later_version status: public - id: '21021' relation: dissertation_contains status: public status: public title: Braiding vineyards tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '21291' abstract: - lang: eng text: The complexity and specificity of movement in vertebrates is driven by a rich diversity of spinal motor and interneuron cell types. During development, eleven spinal cord progenitor domains generate an equivalent number of cardinal neuron types. How progenitor domains, individual progenitors, and post-mitotic diversity relate is still unknown. We performed high-resolution, single-progenitor cell lineage tracing in the embryonic mouse spinal cord using mosaic analysis with double markers (MADM). Our quantitative study of lineage progression revealed that spinal cord progenitors undergo highly variable numbers of proliferative, neurogenic, and gliogenic cell divisions. The nascent clonally-related neurons migrate radially over large distances, span the dorsoventral axis, and even cross the midline, demonstrating striking bilaterality. Molecular and morphometric analysis indicate high levels of progenitor multipotency, with an individual progenitor capable of producing several molecularly and morphologically distinct neuron types, as well as astrocytes. These findings redefine spinal cord development as a process in which lineage variability — rather than rigid progenitor identity — drives the generation of cellular diversity. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: "We would like to thank Elizabeth Marin, Anna Kicheva, Igor Adameyko, and James Briscoe as\r\nwell as members of the Sweeney and Hippemeyer labs and SFB consortium for comments on\r\nthe manuscript. We are also grateful for the technical support of the Preclinical and Imaging and\r\nOptics Facilities support teams (ISTA). In addition, we thank our funding sources for providing\r\nthe resources to do these experiments: Horizon Europe ERC Starting Grant Number 101041551\r\n(M.S.; L.B.S.); Special Research Program (SFB) of the Austrian Science Fund (FWF)\r\nNeuroStem Modulation Project numbers F7814-B (S.A.G.; M.S.; G.S.; and L.B.S.) and F7805\r\n(G.C. and S.H.). S.A.G is supported by a Boehringer Ingelheim Fonds PhD Fellowship, F.D.S.N.\r\nby an Institute of Science and Technology Austria (ISTA) GROW fellowship, and G.C. by an\r\nISTA Plus postdoctoral fellowship from the European Commission. S.H./L.B.S. and G.C. were\r\nadditionally supported by institutional funds from the ISTA and the University of Exeter,\r\nrespectively. " article_processing_charge: No author: - first_name: Sophie A full_name: Gobeil, Sophie A id: 2f3e9efb-eb24-11ec-86b2-88efb11d59fa last_name: Gobeil - first_name: Francisco full_name: Da Silveira Neto, Francisco id: 8cfb7412-10a7-11f1-add1-82b44e6418f2 last_name: Da Silveira Neto - first_name: Giulia full_name: Silvestrelli, Giulia id: 12632ae8-799e-11ef-94a2-e5a3b5ef49e9 last_name: Silvestrelli - first_name: Matthijs Geert full_name: Smits, Matthijs Geert id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0 last_name: Smits - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Gobeil SA, Da Silveira Neto F, Silvestrelli G, et al. Lineage origin of spinal cord cell type diversity. bioRxiv. doi:10.64898/2026.02.12.705305 apa: Gobeil, S. A., Da Silveira Neto, F., Silvestrelli, G., Smits, M. G., Streicher, C., Cheung, G. T., … Sweeney, L. B. (n.d.). Lineage origin of spinal cord cell type diversity. bioRxiv. https://doi.org/10.64898/2026.02.12.705305 chicago: Gobeil, Sophie A, Francisco Da Silveira Neto, Giulia Silvestrelli, Matthijs Geert Smits, Carmen Streicher, Giselle T Cheung, Simon Hippenmeyer, and Lora B. Sweeney. “Lineage Origin of Spinal Cord Cell Type Diversity.” BioRxiv, n.d. https://doi.org/10.64898/2026.02.12.705305. ieee: S. A. Gobeil et al., “Lineage origin of spinal cord cell type diversity,” bioRxiv. . ista: Gobeil SA, Da Silveira Neto F, Silvestrelli G, Smits MG, Streicher C, Cheung GT, Hippenmeyer S, Sweeney LB. Lineage origin of spinal cord cell type diversity. bioRxiv, 10.64898/2026.02.12.705305. mla: Gobeil, Sophie A., et al. “Lineage Origin of Spinal Cord Cell Type Diversity.” BioRxiv, doi:10.64898/2026.02.12.705305. short: S.A. Gobeil, F. Da Silveira Neto, G. Silvestrelli, M.G. Smits, C. Streicher, G.T. Cheung, S. Hippenmeyer, L.B. Sweeney, BioRxiv (n.d.). corr_author: '1' date_created: 2026-02-17T11:36:20Z date_published: 2026-02-16T00:00:00Z date_updated: 2026-04-14T08:16:55Z day: '16' ddc: - '570' department: - _id: SiHi - _id: LoSw doi: 10.64898/2026.02.12.705305 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.64898/2026.02.12.705305 month: '02' oa: 1 oa_version: Preprint project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e grant_number: F7814 name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity' - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: bioRxiv publication_status: submitted status: public title: Lineage origin of spinal cord cell type diversity tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- OA_place: repository OA_type: green _id: '21134' abstract: - lang: eng text: "The Nakamoto consensus protocol underlying the Bitcoin blockchain uses proof of work as a voting mechanism. Honest miners who contribute hashing power towards securing the chain try to extend the longest chain they are aware of. Despite its simplicity, Nakamoto consensus achieves meaningful security guarantees assuming that at any point in time, a majority of the hashing power is controlled by honest parties. This also holds under “resource variability”, i.e., if the total hashing power varies greatly over time.\r\nProofs of space (PoSpace) have been suggested as a more sustainable replacement for proofs of work. Unfortunately, no construction of a “longest-chain” blockchain based on PoSpace, that is secure under dynamic availability, is known. In this work, we prove that without additional assumptions no such protocol exists. We exactly quantify this impossibility result by proving a bound on the length of the fork required for double spending as a function of the adversarial capabilities. This bound holds for any chain selection rule, and we also show a chain selection rule (albeit a very strange one) that almost matches this bound.\r\nThe Nakamoto consensus protocol underlying the Bitcoin blockchain uses proof of work as a voting mechanism. Honest miners who contribute hashing power towards securing the chain try to extend the longest chain they are aware of. Despite its simplicity, Nakamoto consensus achieves meaningful security guarantees assuming that at any point in time, a majority of the hashing power is controlled by honest parties. This also holds under “resource variability”, i.e., if the total hashing power varies greatly over time.\r\n\r\nProofs of space (PoSpace) have been suggested as a more sustainable replacement for proofs of work. Unfortunately, no construction of a “longest-chain” blockchain based on PoSpace, that is secure under dynamic availability, is known. In this work, we prove that without additional assumptions no such protocol exists. We exactly quantify this impossibility result by proving a bound on the length of the fork required for double spending as a function of the adversarial capabilities. This bound holds for any chain selection rule, and we also show a chain selection rule (albeit a very strange one) that almost matches this bound.\r\n\r\nConcretely, we consider a security game in which the honest parties at any point control 0 > 1\r\n times more space than the adversary. The adversary can change the honest space by a factor 1+- E with every block (dynamic availability), and “replotting” the space (which allows answering two challenges using the same space) takes as much time as p blocks.\r\nWe prove that no matter what chain selection rule is used, in this game the adversary can create a fork of length o^2 . p/E that will be picked as the winner by the chain selection rule.\r\nWe also provide an upper bound that matches the lower bound up to a factor o. There exists a chain selection rule (albeit a very strange one) which in the above game requires forks of length at least o . p/E\r\nOur results show the necessity of additional assumptions to create a secure PoSpace based longest-chain blockchain. The Chia network in addition to PoSpace uses a verifiable delay function. Our bounds show that an additional primitive like that is necessary." acknowledgement: This research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/F85. alternative_title: - LNCS article_processing_charge: No arxiv: 1 author: - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Baig MA, Pietrzak KZ. On the (in)security of Proofs-of-space based longest-chain blockchains. In: 29th International Conference on Financial Cryptography and Data Security. Vol 15752. Springer Nature; 2026:127-142. doi:10.1007/978-3-032-07035-7_8' apa: 'Baig, M. A., & Pietrzak, K. Z. (2026). On the (in)security of Proofs-of-space based longest-chain blockchains. In 29th International Conference on Financial Cryptography and Data Security (Vol. 15752, pp. 127–142). Miyakojima, Japan: Springer Nature. https://doi.org/10.1007/978-3-032-07035-7_8' chicago: Baig, Mirza Ahad, and Krzysztof Z Pietrzak. “On the (in)Security of Proofs-of-Space Based Longest-Chain Blockchains.” In 29th International Conference on Financial Cryptography and Data Security, 15752:127–42. Springer Nature, 2026. https://doi.org/10.1007/978-3-032-07035-7_8. ieee: M. A. Baig and K. Z. Pietrzak, “On the (in)security of Proofs-of-space based longest-chain blockchains,” in 29th International Conference on Financial Cryptography and Data Security, Miyakojima, Japan, 2026, vol. 15752, pp. 127–142. ista: 'Baig MA, Pietrzak KZ. 2026. On the (in)security of Proofs-of-space based longest-chain blockchains. 29th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 15752, 127–142.' mla: Baig, Mirza Ahad, and Krzysztof Z. Pietrzak. “On the (in)Security of Proofs-of-Space Based Longest-Chain Blockchains.” 29th International Conference on Financial Cryptography and Data Security, vol. 15752, Springer Nature, 2026, pp. 127–42, doi:10.1007/978-3-032-07035-7_8. short: M.A. Baig, K.Z. Pietrzak, in:, 29th International Conference on Financial Cryptography and Data Security, Springer Nature, 2026, pp. 127–142. conference: end_date: 2025-04-18 location: Miyakojima, Japan name: 'FC: Financial Cryptography and Data Security' start_date: 2025-04-14 corr_author: '1' date_created: 2026-02-01T23:01:43Z date_published: 2026-01-01T00:00:00Z date_updated: 2026-04-15T08:45:18Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-032-07035-7_8 external_id: arxiv: - '2505.14891' intvolume: ' 15752' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2505.14891 month: '01' oa: 1 oa_version: Preprint page: 127-142 project: - _id: 34a34d57-11ca-11ed-8bc3-a2688a8724e1 grant_number: F8509 name: Security and Privacy by Design for Complex Systems publication: 29th International Conference on Financial Cryptography and Data Security publication_identifier: eissn: - 1611-3349 isbn: - '9783032070340' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '21651' relation: dissertation_contains status: public scopus_import: '1' status: public title: On the (in)security of Proofs-of-space based longest-chain blockchains type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15752 year: '2026' ... --- OA_place: publisher _id: '21651' abstract: - lang: eng text: "Blockchains enable distributed consensus in permissionless settings, where participants\r\nare unknown, dynamically changing, and do not trust each other. While Bitcoin,\r\nbased on Proof-of-Work (PoW), was the first protocol in this model, significant\r\nresearch has focused on permissionless protocols using alternative physical resources,\r\nspecifically Proof-of-Space (PoSpace) and Verifiable Delay Functions (VDFs). This\r\nthesis investigates the theoretical limits and design space of longest-chain protocols in\r\nthe fully permissionless and dynamically available settings using these three resources.\r\nFirst, we address the feasibility of blockchains relying solely on storage as a resource.\r\nWe prove a fundamental impossibility result: there exists no secure longest-chain\r\nprotocol based exclusively on Proof-of-Space in the fully permissionless or dynamically\r\navailable settings. Further, we quantify the adversarial capabilities required to execute\r\na double-spend attack. Our result formally justifies the necessity of coupling PoSpace\r\nwith time-dependent primitives (such as VDFs) or to move to less permissive settings\r\n(quasi-permissionless or permissioned) to ensure security.\r\nSecond, we generalize Nakamoto-like heaviest chain consensus to protocols utilizing\r\ncombinations of multiple physical resources. We analyze chain selection rules governed\r\nby a weight function Γ(S, V,W), which assigns weight to blocks based on recorded\r\nSpace (S), VDF speed (V ), and Work (W). We provide a complete classification\r\nof secure weight functions, proving that a weight function is secure against private\r\ndouble-spend attacks if and only if it is homogeneous in the timed resources (V,W)\r\nand sub-homogeneous in S. This framework unifies existing protocols like Bitcoin and\r\nChia under a single theoretical model and provides a powerful tool for designing new\r\nlongest-chain blockchains from a mix of physical resources." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig citation: ama: Baig MA. On secure chain selection rules from physical resources in a permissionless setting. 2026. doi:10.15479/AT-ISTA-21651 apa: Baig, M. A. (2026). On secure chain selection rules from physical resources in a permissionless setting. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21651 chicago: Baig, Mirza Ahad. “On Secure Chain Selection Rules from Physical Resources in a Permissionless Setting.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21651. ieee: M. A. Baig, “On secure chain selection rules from physical resources in a permissionless setting,” Institute of Science and Technology Austria, 2026. ista: Baig MA. 2026. On secure chain selection rules from physical resources in a permissionless setting. Institute of Science and Technology Austria. mla: Baig, Mirza Ahad. On Secure Chain Selection Rules from Physical Resources in a Permissionless Setting. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21651. short: M.A. Baig, On Secure Chain Selection Rules from Physical Resources in a Permissionless Setting, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-04-02T09:31:34Z date_published: 2026-03-04T00:00:00Z date_updated: 2026-04-15T08:45:19Z day: '04' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/AT-ISTA-21651 file: - access_level: closed checksum: c3986dba90653dac97adba662ebff238 content_type: application/x-zip-compressed creator: mbaig date_created: 2026-04-03T17:28:48Z date_updated: 2026-04-13T08:24:13Z file_id: '21655' file_name: PhD-Thesis-Mirza-Ahad-Baig - Library Submission.zip file_size: 139353434 relation: source_file - access_level: open_access checksum: 292a5989262521f7c145a109d1f348cb content_type: application/pdf creator: mbaig date_created: 2026-04-03T17:29:30Z date_updated: 2026-04-15T07:37:25Z file_id: '21656' file_name: 2026_Baig_Mirza_Ahad_Thesis.pdf file_size: 1942037 relation: main_file file_date_updated: 2026-04-15T07:37:25Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication_identifier: isbn: - 978-3-99078-078-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21134' relation: part_of_dissertation status: public - id: '20587' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: On secure chain selection rules from physical resources in a permissionless setting tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '20991' abstract: - lang: eng text: "Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms." acknowledgement: "I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Diego Fernando full_name: Garcia Castillo, Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo citation: ama: Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:10.15479/AT-ISTA-20991 apa: Garcia Castillo, D. F. (2026). The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20991 chicago: Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20991. ieee: D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026. ista: Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. mla: Garcia Castillo, Diego Fernando. The Genomic Architecture of Local Adaptation in Introduced Populations. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20991. short: D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-01-16T09:47:59Z date_published: 2026-01-16T00:00:00Z date_updated: 2026-04-16T12:20:37Z day: '16' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20991 file: - access_level: closed checksum: 841f1bc073d667125729b2a017f8c37a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20996' file_name: 2026_Garcia_Diego_Thesis.docx file_size: 22456421 relation: source_file - access_level: open_access checksum: a1f33d4f183ce7072eee42a6ccf5340b content_type: application/pdf creator: dgarciac date_created: 2026-01-16T12:25:13Z date_updated: 2026-01-16T12:25:13Z file_id: '20997' file_name: 2026_Garcia_Diego_Thesis.pdf file_size: 9556719 relation: main_file success: 1 - access_level: closed checksum: 98a80691067174c30fe53f38ce7344e6 content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z description: Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis. file_id: '20998' file_name: 2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar file_size: 54491433 relation: supplementary_material - access_level: open_access checksum: 99a3cab2fa36666b9a92eefc27d586da content_type: application/x-compressed creator: dgarciac date_created: 2026-01-16T13:08:14Z date_updated: 2026-01-16T13:08:14Z file_id: '20999' file_name: 2026_DiegoGarcia_Thesis-Supplementary_Material.rar file_size: 7982811 relation: supplementary_material - access_level: open_access checksum: 255fdf56b2932c46bf27c63aa6106a4f content_type: text/plain creator: dgarciac date_created: 2026-01-16T13:08:59Z date_updated: 2026-01-16T13:08:59Z file_id: '21000' file_name: README.txt file_size: 732 relation: supplementary_material file_date_updated: 2026-01-16T13:08:59Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '199' publication_identifier: isbn: - 978-3-99078-077-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18498' relation: research_data status: public - id: '18491' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 title: The genomic architecture of local adaptation in introduced populations tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2026' ... --- OA_type: closed access _id: '21765' abstract: - lang: eng text: "Dielectric particles of the same material exchange electrical charge during collisions or sliding contacts, yet the underlying charge-exchange mechanism is still not understood. The fact that particles can become highly charged as a result of this effect has significant consequences for many settings, both in nature and industry, such as thunderstorms, volcanic eruptions, particle aggregation during meteorite and planet formation, and the clogging of industrial granular systems. Toward understanding these systems, great efforts have been made to develop precise in situ measurements for particle charge, e.g., to determine ensemble charge distributions or measure exchange during individual contacts. Here, we present experimental results concerning the particle size scaling of the stationary-state charge distributions of oxide particles in the sub-millimeter range. We measure the charge distributions for large ensembles of monodisperse ZrO2:SiO2 composite spheres, ranging from 172 to 545µ⁢m in diameter. These distributions are non-Gaussian and collapse to a single master curve when plotted as functions of the surface charge density Σ=\U0001D45E/4⁢\U0001D70B⁢\U0001D4452. X-ray fluorescence and atomic force microscopy measurements show that the differences in the measured charge distributions are not due to variations in chemical composition or surface roughness, but rather to size alone. Our findings provide constraints on microscopic models for charge exchange, namely that they should lead to steady-state distributions that are non-Gaussian and scale in a specific way with particle size." acknowledgement: This research was supported by ANID Grants QUIMAL No. 160001, FONDECYT No. 1221597, and FONDEQUIP No. EQM190177. The authors thank Rodrigo Espinoza for the EDS-SEM measurements and Domingo Jullian for fruitful discussions. We also acknowledge the technical assistance of Ricardo Silva and Andrés Espinosa at DFI, FCFM, Universidad de Chile. article_number: '045604' article_processing_charge: No article_type: original author: - first_name: Macarena full_name: Lara, Macarena last_name: Lara - first_name: Marcos full_name: Flores, Marcos last_name: Flores - first_name: Gustavo full_name: Castillo, Gustavo last_name: Castillo - first_name: Santiago full_name: Tassara, Santiago last_name: Tassara - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Nicolás full_name: Mujica, Nicolás last_name: Mujica citation: ama: Lara M, Flores M, Castillo G, Tassara S, Waitukaitis SR, Mujica N. Particle size scaling of non-Gaussian granular charge distributions. Physical Review Materials. 2026;10(4). doi:10.1103/qw6t-xqdw apa: Lara, M., Flores, M., Castillo, G., Tassara, S., Waitukaitis, S. R., & Mujica, N. (2026). Particle size scaling of non-Gaussian granular charge distributions. Physical Review Materials. American Physical Society. https://doi.org/10.1103/qw6t-xqdw chicago: Lara, Macarena, Marcos Flores, Gustavo Castillo, Santiago Tassara, Scott R Waitukaitis, and Nicolás Mujica. “Particle Size Scaling of Non-Gaussian Granular Charge Distributions.” Physical Review Materials. American Physical Society, 2026. https://doi.org/10.1103/qw6t-xqdw. ieee: M. Lara, M. Flores, G. Castillo, S. Tassara, S. R. Waitukaitis, and N. Mujica, “Particle size scaling of non-Gaussian granular charge distributions,” Physical Review Materials, vol. 10, no. 4. American Physical Society, 2026. ista: Lara M, Flores M, Castillo G, Tassara S, Waitukaitis SR, Mujica N. 2026. Particle size scaling of non-Gaussian granular charge distributions. Physical Review Materials. 10(4), 045604. mla: Lara, Macarena, et al. “Particle Size Scaling of Non-Gaussian Granular Charge Distributions.” Physical Review Materials, vol. 10, no. 4, 045604, American Physical Society, 2026, doi:10.1103/qw6t-xqdw. short: M. Lara, M. Flores, G. Castillo, S. Tassara, S.R. Waitukaitis, N. Mujica, Physical Review Materials 10 (2026). date_created: 2026-04-26T22:01:47Z date_published: 2026-04-01T00:00:00Z date_updated: 2026-04-28T07:13:56Z day: '01' department: - _id: ScWa doi: 10.1103/qw6t-xqdw intvolume: ' 10' issue: '4' language: - iso: eng month: '04' oa_version: None publication: Physical Review Materials publication_identifier: eissn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Particle size scaling of non-Gaussian granular charge distributions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21485' abstract: - lang: eng text: Insulating oxides are among the most abundant solid materials in the universe1,2,3. Of the many ways in which they influence natural phenomena, perhaps the most consequential is their capacity to transfer electrical charge during contact4,5,6,7,8,9,10—which occurs even between samples of the same oxide—yet the symmetry-breaking parameter that causes this remains unidentified11,12. Here we show that adventitious carbonaceous molecules adsorbed from the environment are the symmetry-breaking factor in same-material oxide contact electrification (CE). We use acoustic levitation to measure charge exchange between a sphere and a plate composed of identical amorphous silicon dioxide (SiO2). Although charging polarity is random for co-prepared samples, we control it with baking or plasma treatment. Observing the charge-exchange relaxation afterwards, we see dynamics over a timescale of hours and connect this directly to the presence of adventitious carbon with time-of-flight mass spectrometry, low-energy ion scattering and infrared spectroscopy. Going further, we confirm that adventitious carbon can even determine charge exchange among different oxides. Our results identify the symmetry-breaking parameter that causes insulating oxides to exchange charge in settings ranging from desert sands4 to volcanic plumes5,6, while simultaneously highlighting an overlooked factor in CE more broadly. acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: ScienComp - _id: LifeSc acknowledgement: This project has received support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 949120) and from the Marie Skłodowska-Curie programme (grant agreement no. 754411). We acknowledge the state of Lower Austria and the European Regional Development Fund under grant no. WST3-F-542638/004-2021. N.M. acknowledges support from grant Fondecyt 1221597. G.G. is a Serra Húnter fellow. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility and Lab Support Facility. We thank the Modic group for the use of the Laue camera, T. Zauner for the photography of the experimental set-up and R. Möller for insightful discussions. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Galien M full_name: Grosjean, Galien M id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425 last_name: Grosjean orcid: 0000-0001-5154-417X - first_name: Markus full_name: Ostermann, Markus last_name: Ostermann - first_name: Markus full_name: Sauer, Markus last_name: Sauer - first_name: Michael full_name: Hahn, Michael last_name: Hahn - first_name: Christian M. full_name: Pichler, Christian M. last_name: Pichler - first_name: Florian full_name: Fahrnberger, Florian last_name: Fahrnberger - first_name: Felix full_name: Pertl, Felix id: 6313aec0-15b2-11ec-abd3-ed67d16139af last_name: Pertl orcid: 0000-0003-0463-5794 - first_name: Daniel full_name: Balazs, Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - first_name: Mason M. full_name: Link, Mason M. last_name: Link - first_name: Seong H. full_name: Kim, Seong H. last_name: Kim - first_name: Devin L. full_name: Schrader, Devin L. last_name: Schrader - first_name: Adriana full_name: Blanco, Adriana last_name: Blanco - first_name: Francisco full_name: Gracia, Francisco last_name: Gracia - first_name: Nicolás full_name: Mujica, Nicolás last_name: Mujica - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Grosjean GM, Ostermann M, Sauer M, et al. Adventitious carbon breaks symmetry in oxide contact electrification. Nature. 2026;651(8106):626-631. doi:10.1038/s41586-025-10088-w apa: Grosjean, G. M., Ostermann, M., Sauer, M., Hahn, M., Pichler, C. M., Fahrnberger, F., … Waitukaitis, S. R. (2026). Adventitious carbon breaks symmetry in oxide contact electrification. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-10088-w chicago: Grosjean, Galien M, Markus Ostermann, Markus Sauer, Michael Hahn, Christian M. Pichler, Florian Fahrnberger, Felix Pertl, et al. “Adventitious Carbon Breaks Symmetry in Oxide Contact Electrification.” Nature. Springer Nature, 2026. https://doi.org/10.1038/s41586-025-10088-w. ieee: G. M. Grosjean et al., “Adventitious carbon breaks symmetry in oxide contact electrification,” Nature, vol. 651, no. 8106. Springer Nature, pp. 626–631, 2026. ista: Grosjean GM, Ostermann M, Sauer M, Hahn M, Pichler CM, Fahrnberger F, Pertl F, Balazs D, Link MM, Kim SH, Schrader DL, Blanco A, Gracia F, Mujica N, Waitukaitis SR. 2026. Adventitious carbon breaks symmetry in oxide contact electrification. Nature. 651(8106), 626–631. mla: Grosjean, Galien M., et al. “Adventitious Carbon Breaks Symmetry in Oxide Contact Electrification.” Nature, vol. 651, no. 8106, Springer Nature, 2026, pp. 626–31, doi:10.1038/s41586-025-10088-w. short: G.M. Grosjean, M. Ostermann, M. Sauer, M. Hahn, C.M. Pichler, F. Fahrnberger, F. Pertl, D. Balazs, M.M. Link, S.H. Kim, D.L. Schrader, A. Blanco, F. Gracia, N. Mujica, S.R. Waitukaitis, Nature 651 (2026) 626–631. corr_author: '1' date_created: 2026-03-23T15:04:00Z date_published: 2026-03-18T00:00:00Z date_updated: 2026-04-28T12:06:01Z day: '18' ddc: - '540' department: - _id: ScWa - _id: GradSch - _id: LifeSc doi: 10.1038/s41586-025-10088-w ec_funded: 1 external_id: pmid: - '41851325' file: - access_level: open_access checksum: dafef9ed575b44be4263e948a47ae056 content_type: application/pdf creator: dernst date_created: 2026-03-24T06:57:08Z date_updated: 2026-03-24T06:57:08Z file_id: '21494' file_name: 2026_Nature_Grosjean.pdf file_size: 12245694 relation: main_file success: 1 file_date_updated: 2026-03-24T06:57:08Z has_accepted_license: '1' intvolume: ' 651' issue: '8106' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 626-631 pmid: 1 project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/colliding-dust-and-the-sparks-of-creation/ status: public title: Adventitious carbon breaks symmetry in oxide contact electrification tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 651 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21015' abstract: - lang: eng text: Early embryo geometry is one of the most invariant species-specific traits, yet its role in ensuring developmental reproducibility and robustness remains underexplored. Here we show that in zebrafish, the geometry of the fertilized egg—specifically its curvature and volume—serves as a critical initial condition triggering a cascade of events that influence development. The embryo geometry guides patterned asymmetric cell divisions in the blastoderm, generating radial gradients of cell volume and nucleocytoplasmic ratio. These gradients generate mitotic phase waves, with the nucleocytoplasmic ratio determining individual cell cycle periods independently of other cells. We demonstrate that reducing cell autonomy reshapes these waves, emphasizing the instructive role of geometry-derived volume patterns in setting the intrinsic period of the cell cycle oscillator. In addition to organizing cell cycles, early embryo geometry spatially patterns zygotic genome activation at the midblastula transition, a key step in establishing embryonic autonomy. Disrupting the embryo shape alters the zygotic genome activation pattern and causes ectopic germ layer specification, underscoring the developmental significance of geometry. Together, our findings reveal a symmetry-breaking function of early embryo geometry in coordinating cell cycle and transcriptional patterning. acknowledged_ssus: - _id: PreCl - _id: Bio - _id: ScienComp - _id: LifeSc acknowledgement: We thank N. Petridou (EMBL) for sharing results before publication. N.M. was supported by funding from the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie COFUND Actions ISTplus grant agreement number 754411. Y.I.L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. The research was supported by funding to C.-P.H. from the NOMIS Foundation, Project ID 1.844. We would like to thank past and present members of the Heisenberg and Hannezo groups for discussions, particularly S. Shamipour, V. Doddihal, M. Jovic, N. Hino, F. N. Arslan, R. Kobylinska and C. Camelo for feedback on the draft manuscript. This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria through resources provided by the Aquatics Facility, Imaging & Optics Facility (IOF), Scientific Computing (SciComp) facility and Lab Support Facility (LSF). Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Nikhil full_name: Mishra, Nikhil id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E last_name: Mishra orcid: 0000-0002-6425-5788 - first_name: Yuting I full_name: Li, Yuting I id: ee7a5ca8-8b71-11ed-b662-b3341c05b7eb last_name: Li - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. 2026;22:139-150. doi:10.1038/s41567-025-03122-1 apa: Mishra, N., Li, Y. I., Hannezo, E. B., & Heisenberg, C.-P. J. (2026). Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03122-1 chicago: Mishra, Nikhil, Yuting I Li, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-025-03122-1. ieee: N. Mishra, Y. I. Li, E. B. Hannezo, and C.-P. J. Heisenberg, “Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo,” Nature Physics, vol. 22. Springer Nature, pp. 139–150, 2026. ista: Mishra N, Li YI, Hannezo EB, Heisenberg C-PJ. 2026. Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo. Nature Physics. 22, 139–150. mla: Mishra, Nikhil, et al. “Geometry-Driven Asymmetric Cell Divisions Pattern Cell Cycles and Zygotic Genome Activation in the Zebrafish Embryo.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 139–50, doi:10.1038/s41567-025-03122-1. short: N. Mishra, Y.I. Li, E.B. Hannezo, C.-P.J. Heisenberg, Nature Physics 22 (2026) 139–150. corr_author: '1' date_created: 2026-01-20T10:12:19Z date_published: 2026-01-05T00:00:00Z date_updated: 2026-04-28T12:55:30Z day: '05' ddc: - '570' department: - _id: EdHa - _id: CaHe doi: 10.1038/s41567-025-03122-1 ec_funded: 1 external_id: oaworkid: - W7118187193 file: - access_level: open_access checksum: 0ab7ac2fbcb61a364dba57152db64ed7 content_type: application/pdf creator: dernst date_created: 2026-01-21T08:21:11Z date_updated: 2026-01-21T08:21:11Z file_id: '21026' file_name: 2026_NaturePhysics_Mishra.pdf file_size: 7335694 relation: main_file success: 1 file_date_updated: 2026-01-21T08:21:11Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '01' oa: 1 oa_version: Published Version oaworkid: 1 page: 139-150 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: 917c023a-16d5-11f0-9cad-eb5cafc52090 name: Cytoplasmic self-organization into cell-like compartments as a common guiding principle in early animal development publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 issnl: - ' 1745-2473' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: research_data url: https://ista.ac.at/en/news/geometry-shapes-life/ scopus_import: '1' status: public title: Geometry-driven asymmetric cell divisions pattern cell cycles and zygotic genome activation in the zebrafish embryo tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 22 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21382' abstract: - lang: eng text: The exceptional energy-harvesting efficiency of lead-halide perovskites arises from unusually long photocarrier diffusion lengths and recombination lifetimes that persist even in defect-rich, solution-grown samples. Paradoxically, perovskites are also known for having very short exciton decay times. Here, we resolve this apparent contradiction by showing that key optoelectronic properties of perovskites can be explained by localized flexoelectric polarization confined to interfaces between domains of spontaneous strain. Using birefringence imaging, electrochemical staining, and zero-bias photocurrent measurements, we visualize the domain structure and directly probe the associated internal fields in nominally cubic single crystals of methylammonium lead bromide. We demonstrate that localized flexoelectric fields spatially separate electrons and holes to opposite sides of domain walls, exponentially suppressing recombination. Domain walls thus act as efficient mesoscopic transport channels for long-lived photocarriers, microscopically linking structural heterogeneity to charge transport and offering mechanistically informed design principles for perovskite solar-energy technologies. acknowledged_ssus: - _id: Bio - _id: M-Shop acknowledgement: We are grateful to A. G. Volosniev for the valuable discussions. We thank D. Milius for the assistance with microscopy. D. R. would like to thank F. Filakovský and T. Čuchráč for the valuable discussions. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF) and the Miba Machine Shop Facility (MS). article_number: '946' article_processing_charge: Yes article_type: original author: - first_name: Dmytro full_name: Rak, Dmytro id: 70313b46-47c2-11ec-9e88-cd79101918fe last_name: Rak - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Daniel full_name: Balazs, Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - first_name: Ayan A. full_name: Zhumekenov, Ayan A. last_name: Zhumekenov - first_name: Osman M. full_name: Bakr, Osman M. last_name: Bakr - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Rak D, Lorenc D, Balazs D, Zhumekenov AA, Bakr OM, Alpichshev Z. Flexoelectric domain walls enable charge separation and transport in cubic perovskites. Nature Communications. 2026;17. doi:10.1038/s41467-026-68660-5 apa: Rak, D., Lorenc, D., Balazs, D., Zhumekenov, A. A., Bakr, O. M., & Alpichshev, Z. (2026). Flexoelectric domain walls enable charge separation and transport in cubic perovskites. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-026-68660-5 chicago: Rak, Dmytro, Dusan Lorenc, Daniel Balazs, Ayan A. Zhumekenov, Osman M. Bakr, and Zhanybek Alpichshev. “Flexoelectric Domain Walls Enable Charge Separation and Transport in Cubic Perovskites.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-68660-5. ieee: D. Rak, D. Lorenc, D. Balazs, A. A. Zhumekenov, O. M. Bakr, and Z. Alpichshev, “Flexoelectric domain walls enable charge separation and transport in cubic perovskites,” Nature Communications, vol. 17. Springer Nature, 2026. ista: Rak D, Lorenc D, Balazs D, Zhumekenov AA, Bakr OM, Alpichshev Z. 2026. Flexoelectric domain walls enable charge separation and transport in cubic perovskites. Nature Communications. 17, 946. mla: Rak, Dmytro, et al. “Flexoelectric Domain Walls Enable Charge Separation and Transport in Cubic Perovskites.” Nature Communications, vol. 17, 946, Springer Nature, 2026, doi:10.1038/s41467-026-68660-5. short: D. Rak, D. Lorenc, D. Balazs, A.A. Zhumekenov, O.M. Bakr, Z. Alpichshev, Nature Communications 17 (2026). corr_author: '1' date_created: 2026-03-02T10:06:58Z date_published: 2026-02-16T00:00:00Z date_updated: 2026-04-28T12:12:46Z day: '16' ddc: - '530' department: - _id: ZhAl - _id: LifeSc doi: 10.1038/s41467-026-68660-5 external_id: pmid: - '41698893' file: - access_level: open_access checksum: dd7a98de892d0b5abefca7e290ca0f77 content_type: application/pdf creator: dernst date_created: 2026-03-02T14:27:56Z date_updated: 2026-03-02T14:27:56Z file_id: '21390' file_name: 2026_NatureComm_Rak.pdf file_size: 2570918 relation: main_file success: 1 file_date_updated: 2026-03-02T14:27:56Z has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/explaining-next-generation-solar-cells/ scopus_import: '1' status: public title: Flexoelectric domain walls enable charge separation and transport in cubic perovskites tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 17 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21759' abstract: - lang: eng text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges.' acknowledgement: "We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant 101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European Molecular Biology Laboratory (N.O.B., J.C.)." article_number: '102472' article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Elia full_name: Mascolo, Elia id: 776a6ed0-a053-11f0-8635-80b95e0e0d53 last_name: Mascolo orcid: 0000-0003-2977-7844 - first_name: Reka E full_name: Körei, Reka E id: 50FDE43E-AA30-11E9-A72B-8A12E6697425 last_name: Körei - first_name: Noa O. full_name: Borst, Noa O. last_name: Borst - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 2026;98. doi:10.1016/j.gde.2026.102472' apa: 'Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., & Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2026.102472' chicago: 'Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” Current Opinion in Genetics and Development. Elsevier, 2026. https://doi.org/10.1016/j.gde.2026.102472.' ieee: 'E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,” Current Opinion in Genetics and Development, vol. 98. Elsevier, 2026.' ista: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 98, 102472.' mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” Current Opinion in Genetics and Development, vol. 98, 102472, Elsevier, 2026, doi:10.1016/j.gde.2026.102472.' short: E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current Opinion in Genetics and Development 98 (2026). corr_author: '1' date_created: 2026-04-26T22:01:46Z date_published: 2026-04-15T00:00:00Z date_updated: 2026-04-28T12:41:00Z day: '15' department: - _id: GaTk - _id: NiBa doi: 10.1016/j.gde.2026.102472 intvolume: ' 98' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.gde.2026.102472 month: '04' oa: 1 oa_version: Published Version project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Current Opinion in Genetics and Development publication_identifier: eissn: - 1879-0380 issn: - 0959-437X publication_status: epub_ahead publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 98 year: '2026' ... --- OA_type: closed access _id: '21762' abstract: - lang: eng text: Bacteria, like eukaryotes, use conserved cytoskeletal systems for intracellular organization. The plasmid-encoded ParMRC system forms actin-like filaments that segregate low–copy number plasmids. In multicellular cyanobacteria such as Anabaena sp., we found that a chromosomally encoded ParMR system has evolved into a cytoskeletal system named CorMR with a function in cell shape control rather than DNA segregation. Live-cell imaging, in vitro reconstitution, and cryo–electron microscopy revealed that CorM formed dynamically unstable, antiparallel double-stranded filaments that were recruited to the membrane by CorR through an amphipathic helix conserved in multicellular cyanobacteria. CorMR filaments were regulated by MinC, which excluded them from the poles and division plane. Comparative genomics indicated that the repurposing of ParMR and Min systems coevolved with cyanobacterial multicellularity, highlighting the evolutionary plasticity of cytoskeletal systems in bacteria. acknowledged_ssus: - _id: Bio - _id: ScienComp - _id: EM-Fac - _id: LifeSc acknowledgement: "We thank all members of the Loose lab at ISTA for helpful discussions; M. Kojic for critical reading of the manuscript; A. Herrero (Sevilla University) for sharing her extensive BACTH plasmid library and other plasmids, as well as cyanobacterial strains; T. Dagan and F. Nies (both Kiel University) for sharing cyanobacterial strains and plasmids and for valuable discussions; N. Sapay and A. Michon for providing the Amphipaseek code, which enabled us to perform our large-scale amphipathic helix screen of cyanobacterial CorR proteins; V.-V. Hodirnau for support in cryo-ET data collection; and J. Hansen for advice about cryo-EM data processing.\r\nThis work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging & Optics Facility (IOF), the Scientific Computing (SciComp), the Electron Microscopy Facility (EMF), and the Lab Support Facility (LSF). This work was funded by the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant 101034413 to B.L.S.); the European Research Council (ERC) of the European Union (grant ActinID 101076260 to F.K.M.S.); the Swiss National Science Foundation (starting grant TMSGI3_226208 to G.L.W.); and the Jean-Jacques et Letitia Lopez-Loreta Foundation (G.L.W.)." article_number: eaea6343 article_processing_charge: No article_type: original author: - first_name: Benjamin L full_name: Springstein, Benjamin L id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083 last_name: Springstein orcid: 0000-0002-3461-5391 - first_name: Manjunath full_name: Javoor, Manjunath id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2 last_name: Javoor orcid: 0000-0003-2311-2112 - first_name: Daniela full_name: Megrian, Daniela last_name: Megrian - first_name: Roman full_name: Hajdu, Roman id: ffab949d-133f-11ed-8f02-94de21ace503 last_name: Hajdu - first_name: Dustin M. full_name: Hanke, Dustin M. last_name: Hanke - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 - first_name: Gregor L. full_name: Weiss, Gregor L. last_name: Weiss - first_name: Florian Km full_name: Schur, Florian Km id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Springstein BL, Javoor M, Megrian D, et al. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. Science. 2026;392(6795). doi:10.1126/science.aea6343 apa: Springstein, B. L., Javoor, M., Megrian, D., Hajdu, R., Hanke, D. M., Zens, B., … Loose, M. (2026). Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. Science. AAAS. https://doi.org/10.1126/science.aea6343 chicago: Springstein, Benjamin L, Manjunath Javoor, Daniela Megrian, Roman Hajdu, Dustin M. Hanke, Bettina Zens, Gregor L. Weiss, Florian KM Schur, and Martin Loose. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” Science. AAAS, 2026. https://doi.org/10.1126/science.aea6343. ieee: B. L. Springstein et al., “Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape,” Science, vol. 392, no. 6795. AAAS, 2026. ista: Springstein BL, Javoor M, Megrian D, Hajdu R, Hanke DM, Zens B, Weiss GL, Schur FK, Loose M. 2026. Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape. Science. 392(6795), eaea6343. mla: Springstein, Benjamin L., et al. “Repurposing of a DNA Segregation Machinery into a Cytoskeletal System Controlling Cell Shape.” Science, vol. 392, no. 6795, eaea6343, AAAS, 2026, doi:10.1126/science.aea6343. short: B.L. Springstein, M. Javoor, D. Megrian, R. Hajdu, D.M. Hanke, B. Zens, G.L. Weiss, F.K. Schur, M. Loose, Science 392 (2026). corr_author: '1' date_created: 2026-04-26T22:01:46Z date_published: 2026-04-16T00:00:00Z date_updated: 2026-04-28T13:29:05Z day: '16' department: - _id: MaLo - _id: FlSc - _id: GradSch - _id: EM-Fac doi: 10.1126/science.aea6343 ec_funded: 1 external_id: pmid: - '41990175' intvolume: ' 392' issue: '6795' language: - iso: eng month: '04' oa_version: None pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: bd980d18-d553-11ed-ba76-ceaa645c97eb grant_number: '101076260' name: A molecular atlas of Actin filament IDentities in the cell motility machinery publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' scopus_import: '1' status: public title: Repurposing of a DNA segregation machinery into a cytoskeletal system controlling cell shape type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 392 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21704' abstract: - lang: eng text: How functional protein sequences are distributed in sequence space is fundamentally important for evolutionary theory and protein design, particularly if a large diversity of protein functions are hidden in evolutionarily unexplored areas of the sequence space. However, this question is understudied in part because experimental and computational studies use extant sequences as a starting point to study sequence space. Here, we study whether extant sequences are representative of the entire functional sequence space. Across thousands of protein families from vertebrates and bacteria we calculate the dimensionality and the volume of sequence space occupied by extant homologs. We find that the observed dimensionality and volume of extant sequence space are minuscule, many orders of magnitude smaller than what we estimated using a model of protein evolution. Simulating sequence evolution we then quantify the impact of phylogeny, selection, and epistasis on restricting the evolutionary exploration of sequence space. We find that sequence evolution from a single common ancestor, or a single point of origin in sequence space, is by far the largest limiting factor that reduces the dimensionality and volume of extant sequence space. These results indicate that there are vast areas of functional sequence space that have not been explored in evolution because of the excessive restrictions on natural exploration of the protein sequence space imposed by the point of origin effect. We suggest that protein design methods that rely on extant sequences may be limited in their ability to discover truly novel functions. acknowledgement: We thank Olga Kalinina for feedback on our manuscript, Vsevolod Kuksin for fruitful discussions and Lev Tsarin for participation in the design of our models. This work was supported by Japan Science and Technology Agency as part of Adopting Sustainable Partnerships for Innovative Research Ecosystem, Grant No. JPMJAP24B2 (F.A.K. and L.H.I.), and Fonds Zur Förderung der Wissenschaftlichen Forschung Grant ESP253-B (O.O.B.) article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lada H. full_name: Isakova, Lada H. last_name: Isakova - first_name: Elizaveta full_name: Streltsova, Elizaveta id: 57a170da-dc96-11ea-b7c8-ab3565071bf7 last_name: Streltsova - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Peter K. full_name: Vlasov, Peter K. last_name: Vlasov - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Isakova LH, Streltsova E, Bochkareva O, Vlasov PK, Kondrashov F. Descent from a common ancestor restricts exploration of protein sequence space. Proceedings of the National Academy of Sciences. 2026;123(14):e2532018123. doi:10.1073/pnas.2532018123 apa: Isakova, L. H., Streltsova, E., Bochkareva, O., Vlasov, P. K., & Kondrashov, F. (2026). Descent from a common ancestor restricts exploration of protein sequence space. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2532018123 chicago: Isakova, Lada H., Elizaveta Streltsova, Olga Bochkareva, Peter K. Vlasov, and Fyodor Kondrashov. “Descent from a Common Ancestor Restricts Exploration of Protein Sequence Space.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2026. https://doi.org/10.1073/pnas.2532018123. ieee: L. H. Isakova, E. Streltsova, O. Bochkareva, P. K. Vlasov, and F. Kondrashov, “Descent from a common ancestor restricts exploration of protein sequence space,” Proceedings of the National Academy of Sciences, vol. 123, no. 14. National Academy of Sciences, p. e2532018123, 2026. ista: Isakova LH, Streltsova E, Bochkareva O, Vlasov PK, Kondrashov F. 2026. Descent from a common ancestor restricts exploration of protein sequence space. Proceedings of the National Academy of Sciences. 123(14), e2532018123. mla: Isakova, Lada H., et al. “Descent from a Common Ancestor Restricts Exploration of Protein Sequence Space.” Proceedings of the National Academy of Sciences, vol. 123, no. 14, National Academy of Sciences, 2026, p. e2532018123, doi:10.1073/pnas.2532018123. short: L.H. Isakova, E. Streltsova, O. Bochkareva, P.K. Vlasov, F. Kondrashov, Proceedings of the National Academy of Sciences 123 (2026) e2532018123. date_created: 2026-04-12T22:01:47Z date_published: 2026-04-07T00:00:00Z date_updated: 2026-05-04T06:57:31Z day: '07' ddc: - '570' department: - _id: UlWa doi: 10.1073/pnas.2532018123 external_id: pmid: - '41915737' file: - access_level: open_access checksum: 11b7a13a359e302498b2367906093a6b content_type: application/pdf creator: dernst date_created: 2026-05-04T06:46:31Z date_updated: 2026-05-04T06:46:31Z file_id: '21783' file_name: 2026_PNAS_Isakova.pdf file_size: 3355016 relation: main_file success: 1 file_date_updated: 2026-05-04T06:46:31Z has_accepted_license: '1' intvolume: ' 123' issue: '14' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: e2532018123 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Descent from a common ancestor restricts exploration of protein sequence space tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 123 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21746' abstract: - lang: eng text: As vertebrates transitioned from water to land, locomotion shifted from undulatory swimming to limb-based movement. How spinal circuits and their cell types evolved to support this transition remains unclear. We leverage frog metamorphosis, which recapitulates this transition within a single organism, to define how spinal circuits generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons. As limbs develop and their movement complexifies, spinal circuits expand in neuron number and subtype diversity. This expansion is most pronounced for V1 inhibitory neurons, which increase ∼70-fold and diversify into transcriptionally distinct subtypes. Disrupting transcription factors defining emerging motor and V1 populations reveals molecular segregation between swim and limb circuits, highlighting the role of subtype diversity in motor coordination. A multifold increase in inhibitory neuron diversity thus underlies the tail-to-limb locomotor transition, providing a framework for spinal circuit adaptation during vertebrate evolution. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'We would like to thank the members of the Sweeney Lab, Mario de Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript. We are also grateful to Tom Jessell and Chris Kintner for their scientific insight and mentorship during the conception of this project. It would also have not been possible without the technical support of the Aquatics and Imaging and Optics Facility support teams (ISTA). We thank Martin Estermann for preparing the initial draft of the graphical abstract and Niki Barolini for the final version. In addition, we thank our funding sources for providing the resources to do these experiments: GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.), Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858 (to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC) (to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472 (to Z.H.), and Project A.L.S. (to S.B.-M.).' article_number: '117227' article_processing_charge: Yes article_type: original author: - first_name: David full_name: Vijatovic, David id: cf391e77-ec3c-11ea-a124-d69323410b58 last_name: Vijatovic - first_name: 'Florina Alexandra ' full_name: 'Toma, Florina Alexandra ' id: 2f73f876-f128-11eb-9611-b96b5a30cb0e last_name: Toma - first_name: Y full_name: Ignatyev, Y last_name: Ignatyev - first_name: Zoe P full_name: Harrington, Zoe P id: a8144562-32c9-11ee-b5ce-d9800628bda2 last_name: Harrington orcid: 0009-0008-0158-4032 - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Matthijs Geert full_name: Smits, Matthijs Geert id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0 last_name: Smits - first_name: Marco full_name: Dalla Vecchia, Marco id: 02a7a869-ff06-11ed-a87f-86649d6077e5 last_name: Dalla Vecchia - first_name: Alexandra J. full_name: Trevisan, Alexandra J. last_name: Trevisan - first_name: Phillip full_name: Chapman, Phillip last_name: Chapman - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth - first_name: Susan full_name: Brenner-Morton, Susan last_name: Brenner-Morton - first_name: Mariano I. full_name: Gabitto, Mariano I. last_name: Gabitto - first_name: Jeremy S. full_name: Dasen, Jeremy S. last_name: Dasen - first_name: Jay B. full_name: Bikoff, Jay B. last_name: Bikoff - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 2026;45(4). doi:10.1016/j.celrep.2026.117227 apa: Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M., Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2026.117227 chicago: Vijatovic, David, Florina Alexandra Toma, Y Ignatyev, Zoe P Harrington, Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell Reports. Elsevier, 2026. https://doi.org/10.1016/j.celrep.2026.117227. ieee: D. Vijatovic et al., “Multifold increase in spinal inhibitory cell types with emergence of limb movement,” Cell Reports, vol. 45, no. 4. Elsevier, 2026. ista: Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory cell types with emergence of limb movement. Cell Reports. 45(4), 117227. mla: Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell Reports, vol. 45, no. 4, 117227, Elsevier, 2026, doi:10.1016/j.celrep.2026.117227. short: D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild, M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton, M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026). corr_author: '1' date_created: 2026-04-19T22:07:43Z date_published: 2026-04-28T00:00:00Z date_updated: 2026-05-04T12:27:06Z day: '28' ddc: - '570' department: - _id: LoSw - _id: GradSch - _id: TiVo - _id: Bio - _id: NiBa doi: 10.1016/j.celrep.2026.117227 external_id: pmid: - '41964955 ' file: - access_level: open_access checksum: 0d26cdb5b8d8dec3a911d8261a65cdef content_type: application/pdf creator: dernst date_created: 2026-05-04T12:20:10Z date_updated: 2026-05-04T12:20:10Z file_id: '21795' file_name: 2026_CellReports_Vijatovic.pdf file_size: 14925958 relation: main_file success: 1 file_date_updated: 2026-05-04T12:20:10Z has_accepted_license: '1' intvolume: ' 45' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits - _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e grant_number: F7814 name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity' - _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473 grant_number: CZI01 name: Tools for automation and feedback microscopy - _id: bd73af52-d553-11ed-ba76-912049f0ac7a grant_number: FTI21-D-046 name: Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis publication: Cell Reports publication_identifier: eissn: - 2211-1247 issn: - 2639-1856 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Multifold increase in spinal inhibitory cell types with emergence of limb movement tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2026' ...