--- _id: '12723' abstract: - lang: eng text: 'Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.' article_number: '106901' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Abhishek full_name: Shiva Kumar, Abhishek id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a last_name: Shiva Kumar - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Younes full_name: Ashourishokri, Younes id: e32c111f-f6e0-11ea-865d-eb955baea334 last_name: Ashourishokri - 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: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901 apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901 chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901. ieee: A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023. ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901. mla: Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901. short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023). date_created: 2023-03-14T13:11:59Z date_published: 2023-03-10T00:00:00Z date_updated: 2023-08-01T13:39:04Z day: '10' department: - _id: GradSch - _id: ZhAl - _id: MiLe doi: 10.1103/physrevlett.130.106901 external_id: arxiv: - '2203.09443' isi: - '000982435900002' intvolume: ' 130' isi: 1 issue: '10' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2203.09443 month: '03' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Spin-electric coupling in lead halide perovskites type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 130 year: '2023' ... --- _id: '12724' abstract: - lang: eng text: 'We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.' article_number: '125201' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Abhishek full_name: Shiva Kumar, Abhishek id: 5e9a6931-eb97-11eb-a6c2-e96f7058d77a last_name: Shiva Kumar - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Younes full_name: Ashourishokri, Younes id: e32c111f-f6e0-11ea-865d-eb955baea334 last_name: Ashourishokri - first_name: Ayan full_name: Zhumekenov, Ayan last_name: Zhumekenov - first_name: Osman M. full_name: Bakr, Osman M. last_name: Bakr - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201 apa: Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201 chicago: Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201. ieee: A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023. ista: Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201. mla: Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201. short: A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023). date_created: 2023-03-14T13:13:05Z date_published: 2023-03-15T00:00:00Z date_updated: 2023-08-01T13:39:47Z day: '15' department: - _id: GradSch - _id: ZhAl - _id: MiLe doi: 10.1103/physrevb.107.125201 external_id: arxiv: - '2204.04022' isi: - '000972602200006' intvolume: ' 107' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2204.04022 month: '03' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Effective model for studying optical properties of lead halide perovskites type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '12726' abstract: - lang: eng text: "Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex." acknowledged_ssus: - _id: M-Shop - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 citation: ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726 apa: Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726 chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726. ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023. ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria. mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726. short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023. date_created: 2023-03-15T13:22:13Z date_published: 2023-03-23T00:00:00Z date_updated: 2023-11-30T10:55:13Z day: '23' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:12726 file: - access_level: closed checksum: eba0e19fe57a8c15e7aeab55a845efb7 content_type: application/pdf creator: cchlebak date_created: 2023-03-23T12:49:23Z date_updated: 2023-11-24T11:57:46Z description: the main file is missing the bibliography. See new thesis record 14530 for updated files. file_id: '12745' file_name: Thesis_Riedl_2023.pdf file_size: 63734746 relation: main_file - access_level: closed checksum: 0eb7b650cc8ae843bcec7c8a6109ae03 content_type: application/octet-stream creator: cchlebak date_created: 2023-03-23T12:54:34Z date_updated: 2023-09-24T22:30:03Z embargo_to: open_access file_id: '12746' file_name: Thesis_Riedl_2023_source.rar file_size: 339473651 relation: source_file file_date_updated: 2023-11-24T11:57:46Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: None page: '260' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10703' relation: part_of_dissertation status: public - id: '10791' relation: part_of_dissertation status: public - id: '7932' relation: part_of_dissertation status: public - id: '461' relation: part_of_dissertation status: public - id: '14530' relation: new_edition status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Synchronization in collectively moving active matter type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12732' abstract: - lang: eng text: "Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 citation: ama: Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732 apa: Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732 chicago: Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732. ieee: P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023. ista: Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. mla: Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732. short: P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023. date_created: 2023-03-17T13:30:48Z date_published: 2023-03-21T00:00:00Z date_updated: 2023-09-20T10:44:12Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:12732 ec_funded: 1 file: - access_level: closed checksum: 5d2de651ef9449c1b8dc27148ca74777 content_type: application/zip creator: pbrighi date_created: 2023-03-23T16:42:56Z date_updated: 2023-03-23T16:42:56Z file_id: '12753' file_name: Thesis_sub_PBrighi.zip file_size: 42167561 relation: source_file - access_level: open_access checksum: 7caa153d4a5b0873a79358787d2dfe1e content_type: application/pdf creator: pbrighi date_created: 2023-03-23T16:43:14Z date_updated: 2023-03-23T16:43:14Z file_id: '12754' file_name: Thesis_PBrighi.pdf file_size: 13977000 relation: main_file success: 1 file_date_updated: 2023-03-23T16:43:14Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '03' oa: 1 oa_version: None page: '158' project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11470' relation: part_of_dissertation status: public - id: '8308' relation: part_of_dissertation status: public - id: '11469' relation: part_of_dissertation status: public - id: '12750' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: Ergodicity breaking in disordered and kinetically constrained quantum many-body systems 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: '2023' ... --- _id: '12736' abstract: - lang: eng text: Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al. acknowledgement: 'This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.' article_processing_charge: No author: - first_name: Vitaly full_name: Aksenov, Vitaly last_name: Aksenov - first_name: Trevor A full_name: Brown, Trevor A id: 3569F0A0-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov - first_name: Ilya full_name: Kokorin, Ilya last_name: Kokorin citation: ama: Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512 apa: 'Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512' chicago: Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512. ieee: V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440. ista: Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p. mla: Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512. short: V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023. conference: end_date: 2023-03-01 location: Montreal, QB, Canada name: 'PPoPP: Sympopsium on Principles and Practice of Parallel Programming' start_date: 2023-02-25 date_created: 2023-03-19T23:00:58Z date_published: 2023-02-25T00:00:00Z date_updated: 2023-03-20T07:57:27Z day: '25' department: - _id: DaAl - _id: GradSch doi: 10.1145/3572848.3577512 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3572848.3577512 month: '02' oa: 1 oa_version: Published Version page: 438-440 publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming publication_identifier: isbn: - '9798400700156' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Unexpected scaling in path copying trees type: conference_poster user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12762' abstract: - lang: eng text: Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations. acknowledgement: This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Selver full_name: Pepic, Selver id: F93245C4-C3CA-11E9-B4F0-C6F4E5697425 last_name: Pepic - first_name: Oren full_name: Shriki, Oren last_name: Shriki - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9 apa: Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9 chicago: Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9. ieee: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023. ista: Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263. mla: Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9. short: F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263. date_created: 2023-03-26T22:01:08Z date_published: 2023-03-20T00:00:00Z date_updated: 2023-08-16T12:41:53Z day: '20' ddc: - '570' department: - _id: GaTk - _id: GradSch doi: 10.1038/s43588-023-00410-9 ec_funded: 1 external_id: arxiv: - '2108.06686' file: - access_level: open_access checksum: 7c63b2b2edfd68aaffe96d70ca6a865a content_type: application/pdf creator: dernst date_created: 2023-08-16T12:39:57Z date_updated: 2023-08-16T12:39:57Z file_id: '14073' file_name: 2023_NatureCompScience_Lombardi.pdf file_size: 4474284 relation: main_file success: 1 file_date_updated: 2023-08-16T12:39:57Z has_accepted_license: '1' intvolume: ' 3' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version page: 254-263 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism publication: Nature Computational Science publication_identifier: eissn: - 2662-8457 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain 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: 3 year: '2023' ... --- _id: '12781' abstract: - lang: eng text: "Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n" acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vladyslav full_name: Kravchuk, Vladyslav id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87 last_name: Kravchuk citation: ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781 apa: Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781 chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781. ieee: V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023. ista: Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. mla: Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781. short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023. date_created: 2023-03-31T12:24:42Z date_published: 2023-03-23T00:00:00Z date_updated: 2023-08-04T08:54:51Z day: '23' ddc: - '570' - '572' degree_awarded: PhD department: - _id: GradSch - _id: LeSa doi: 10.15479/at:ista:12781 ec_funded: 1 file: - access_level: closed checksum: 5ebb6345cb4119f93460c81310265a6d content_type: application/pdf creator: vkravchu date_created: 2023-04-19T14:33:41Z date_updated: 2023-04-19T14:33:41Z embargo: 2024-04-20 embargo_to: local file_id: '12852' file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf file_size: 6071553 relation: main_file - access_level: closed checksum: c12055c48411d030d2afa51de2166221 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vkravchu date_created: 2023-04-19T14:33:52Z date_updated: 2023-04-20T07:02:59Z embargo: 2024-04-20 embargo_to: local file_id: '12853' file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx file_size: 19468766 relation: source_file file_date_updated: 2023-04-20T07:02:59Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: Published Version page: '127' project: - _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E grant_number: '25541' name: 'Structural characterization of E. coli complex I: an important mechanistic model' - _id: 627abdeb-2b32-11ec-9570-ec31a97243d3 call_identifier: H2020 grant_number: '101020697' name: Structure and mechanism of respiratory chain molecular machines publication_identifier: isbn: - 978-3-99078-029-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12138' relation: part_of_dissertation status: public status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12800' abstract: - lang: eng text: 'The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ' alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth citation: ama: Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800 apa: Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800 chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800. ieee: M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023. ista: Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800. short: M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023. date_created: 2023-04-04T18:57:11Z date_published: 2023-04-05T00:00:00Z date_updated: 2023-06-02T22:30:05Z day: '05' ddc: - '576' degree_awarded: MS department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:12800 file: - access_level: closed checksum: b76cf6d69f2093d8248f6a3f9d4654a4 content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: mjulseth date_created: 2023-04-06T06:09:40Z date_updated: 2023-06-02T22:30:04Z embargo_to: open_access file_id: '12805' file_name: Dispersaldata.xlsx file_size: 52795 relation: supplementary_material - access_level: open_access checksum: 5a13b6d204371572e249f03795bc0d04 content_type: application/vnd.wolfram.nb creator: mjulseth date_created: 2023-04-06T06:11:27Z date_updated: 2023-06-02T22:30:04Z embargo: 2023-06-01 file_id: '12806' file_name: 2023_MSc_ThesisMaraJulseth_Notebook.nb file_size: 787239 relation: supplementary_material - access_level: closed checksum: c3ec842839ed1e66bf2618ae33047df8 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mjulseth date_created: 2023-04-06T08:26:12Z date_updated: 2023-06-02T22:30:04Z embargo_to: open_access file_id: '12812' file_name: ThesisMaraJulseth_04_23.docx file_size: 1061763 relation: source_file - access_level: open_access checksum: 3132cc998fbe3ae2a3a83c2a69367f37 content_type: application/pdf creator: mjulseth date_created: 2023-04-06T08:26:37Z date_updated: 2023-06-02T22:30:04Z embargo: 2023-06-01 file_id: '12813' file_name: ThesisMaraJulseth_04_23.pdf file_size: 1741364 relation: main_file file_date_updated: 2023-06-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '21' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12809' abstract: - lang: eng text: "Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. " acknowledged_ssus: - _id: EM-Fac - _id: Bio - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Catarina full_name: Alcarva, Catarina id: 3A96634C-F248-11E8-B48F-1D18A9856A87 last_name: Alcarva citation: ama: 'Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809' apa: 'Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809' chicago: 'Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.' ieee: 'C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.' ista: 'Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.' mla: 'Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.' short: 'C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.' date_created: 2023-04-06T07:54:09Z date_published: 2023-04-06T00:00:00Z date_updated: 2023-04-26T12:16:56Z day: '06' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:12809 file: - access_level: closed checksum: 35b5997d2b0acb461f9d33d073da0df5 content_type: application/pdf creator: cchlebak date_created: 2023-04-07T06:16:06Z date_updated: 2023-04-07T06:16:06Z embargo: 2024-04-07 embargo_to: open_access file_id: '12814' file_name: Thesis_CatarinaAlcarva_final pdfA.pdf file_size: 9881969 relation: main_file - access_level: closed checksum: 81198f63c294890f6d58e8b29782efdc content_type: application/pdf creator: cchlebak date_created: 2023-04-07T06:17:11Z date_updated: 2023-04-07T06:17:11Z file_id: '12815' file_name: Thesis_CatarinaAlcarva_final_for printing.pdf file_size: 44201583 relation: source_file - access_level: closed checksum: 0317bf7f457bb585f99d453ffa69eb53 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-04-07T06:18:05Z date_updated: 2023-04-07T06:18:05Z file_id: '12816' file_name: Thesis_CatarinaAlcarva_final.docx file_size: 84731244 relation: source_file file_date_updated: 2023-04-07T06:18:05Z has_accepted_license: '1' language: - iso: eng month: '04' oa_version: Published Version page: '115' project: - _id: 267DFB90-B435-11E9-9278-68D0E5697425 name: 'Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: 'Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12826' abstract: - lang: eng text: "During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X citation: ama: Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826 apa: Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826 chicago: Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826. ieee: V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023. ista: Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. mla: Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826. short: V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023. date_created: 2023-04-14T14:56:04Z date_published: 2023-04-18T00:00:00Z date_updated: 2023-06-23T09:47:36Z day: '18' ddc: - '570' - '571' degree_awarded: PhD department: - _id: MaJö - _id: GradSch doi: 10.15479/at:ista:12826 ec_funded: 1 file: - access_level: closed checksum: 5f589a9af025f7eeebfd0c186209913e content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vpokusae date_created: 2023-04-20T09:14:38Z date_updated: 2023-04-20T09:26:51Z file_id: '12857' file_name: Thesis_Pokusaeva.docx file_size: 14507243 relation: source_file - access_level: open_access checksum: bbeed76db45a996b4c91a9abe12ce0ec content_type: application/pdf creator: vpokusae date_created: 2023-04-20T09:14:44Z date_updated: 2023-04-20T09:14:44Z file_id: '12858' file_name: Thesis_Pokusaeva.pdf file_size: 10090711 relation: main_file success: 1 file_date_updated: 2023-04-20T09:26:51Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '106' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: Neural control of optic flow-based navigation in Drosophila melanogaster 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: '2023' ... --- _id: '12846' abstract: - lang: eng text: We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons. acknowledgement: The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA). article_number: '2303.14555' article_processing_charge: No arxiv: 1 author: - first_name: Albert full_name: Chern, Albert last_name: Chern - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida citation: ama: Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555 apa: Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555 chicago: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555. ieee: A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. . ista: Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555. mla: Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555. short: A. Chern, S. Ishida, ArXiv (n.d.). date_created: 2023-04-18T19:16:06Z date_published: 2023-03-25T00:00:00Z date_updated: 2023-04-25T06:51:21Z day: '25' department: - _id: GradSch - _id: ChWo doi: 10.48550/arXiv.2303.14555 external_id: arxiv: - '2303.14555' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2303.14555 month: '03' oa: 1 oa_version: Preprint project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: arXiv publication_status: submitted status: public title: Area formula for spherical polygons via prequantization type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12859' abstract: - lang: eng text: 'Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this "universal" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an "interaction matrix", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10).' acknowledgement: "Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n" alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Simone full_name: Bombari, Simone id: ca726dda-de17-11ea-bc14-f9da834f63aa last_name: Bombari - first_name: Shayan full_name: Kiyani, Shayan id: f5a2b424-e339-11ed-8435-ff3b4fe70cf8 last_name: Kiyani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:2738-2776.' apa: 'Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.' chicago: 'Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In Proceedings of the 40th International Conference on Machine Learning, 202:2738–76. ML Research Press, 2023.' ieee: 'S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.' ista: 'Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.' mla: 'Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.' short: S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776. conference: end_date: 2023-07-29 location: Honolulu, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-04-23T16:11:03Z date_published: 2023-10-27T00:00:00Z date_updated: 2024-09-10T13:03:19Z day: '27' department: - _id: GradSch - _id: MaMo external_id: arxiv: - '2302.01629' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2302.01629 month: '10' oa: 1 oa_version: Preprint page: 2738-2776 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 40th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/simone-bombari/beyond-universal-robustness status: public title: 'Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '12869' abstract: - lang: eng text: 'We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. ' acknowledgement: 'FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ' article_processing_charge: No author: - first_name: Frederik Ravn full_name: Klausen, Frederik Ravn last_name: Klausen - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869' apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869' chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.' ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.' ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.' mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.' short: F.R. Klausen, A.B. Lauritsen, (2023). date_created: 2023-04-26T12:34:49Z date_published: 2023-04-26T00:00:00Z date_updated: 2023-11-13T07:47:29Z day: '26' ddc: - '000' department: - _id: GradSch - _id: RoSe doi: 10.15479/AT:ISTA:12869 file: - access_level: open_access checksum: 85ede12d38bb8d944022a8cba4d719f5 content_type: application/octet-stream creator: alaurits date_created: 2023-04-26T12:30:06Z date_updated: 2023-04-26T12:30:06Z file_id: '12870' file_name: README.md file_size: 4567 relation: main_file success: 1 - access_level: open_access checksum: 25bf79452ae895f9c8a20571a096b4c3 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:27:34Z date_updated: 2023-04-26T12:27:34Z file_id: '12871' file_name: simulations_era=10_flux_varied_europe.zip file_size: 732586731 relation: main_file success: 1 - access_level: open_access checksum: bca48d80ece73eb169aee7211a4a751a content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:29:53Z date_updated: 2023-04-26T12:29:53Z file_id: '12872' file_name: simulations_era=10_flux_varied_torus.zip file_size: 1743893150 relation: main_file success: 1 - access_level: open_access checksum: e77a655db15486a387a36362fbf0b665 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:29:19Z date_updated: 2023-04-26T12:29:19Z file_id: '12873' file_name: simulations_era=10_R_varied_torus.zip file_size: 878391851 relation: main_file success: 1 - access_level: open_access checksum: 8556406513adc4aa2e0417f46680f627 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:30:05Z date_updated: 2023-04-26T12:30:05Z file_id: '12874' file_name: simulations_era=100.zip file_size: 201652478 relation: main_file success: 1 file_date_updated: 2023-04-26T12:30:06Z has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14505' relation: used_in_publication status: for_moderation - id: '12890' relation: used_in_publication status: public status: public title: 'Research data for: A stochastic cellular automaton model of culture formation' tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12885' abstract: - lang: eng text: 'High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ' acknowledged_ssus: - _id: EM-Fac - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 citation: ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885' apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885' chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.' ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.' ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.' mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.' short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-02T07:58:57Z date_published: 2023-04-28T00:00:00Z date_updated: 2023-08-14T07:25:26Z day: '28' ddc: - '546' - '541' degree_awarded: PhD department: - _id: GradSch - _id: MaIb doi: 10.15479/at:ista:12885 ec_funded: 1 file: - access_level: closed checksum: 9347b0e09425f56fdcede5d3528404dc content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mcalcabr date_created: 2023-05-02T07:43:18Z date_updated: 2023-05-02T07:43:18Z file_id: '12887' file_name: Thesis_Calcabrini.docx file_size: 99627036 relation: source_file - access_level: open_access checksum: 2d188b76621086cd384f0b9264b0a576 content_type: application/pdf creator: mcalcabr date_created: 2023-05-02T07:42:45Z date_updated: 2023-05-02T07:42:45Z file_id: '12888' file_name: Thesis_Calcabrini_pdfa.pdf file_size: 8742220 relation: main_file success: 1 file_date_updated: 2023-05-02T07:43:18Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '82' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-028-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10806' relation: part_of_dissertation status: public - id: '10042' relation: part_of_dissertation status: public - id: '12237' relation: part_of_dissertation status: public - id: '9118' relation: part_of_dissertation status: public - id: '10123' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12890' abstract: - lang: eng text: We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders. acknowledgement: Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. article_number: '054307' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Frederik Ravn full_name: Klausen, Frederik Ravn last_name: Klausen - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307 apa: Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.108.054307 chicago: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307. ieee: F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023. ista: Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307. mla: Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307. short: F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023). date_created: 2023-05-04T08:35:01Z date_published: 2023-11-08T00:00:00Z date_updated: 2023-11-13T07:47:30Z day: '08' department: - _id: GradSch - _id: RoSe doi: 10.1103/PhysRevE.108.054307 external_id: arxiv: - '2305.02153' intvolume: ' 108' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2305.02153 month: '11' oa: 1 oa_version: Preprint publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - relation: software url: https://github.com/FrederikRavnKlausen/model-for-culture-formation record: - id: '12869' relation: research_data status: public scopus_import: '1' status: public title: Stochastic cellular automaton model of culture formation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2023' ... --- _id: '12891' abstract: - lang: eng text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 citation: ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891' apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891' chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.' ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.' ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.' mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.' short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-05T08:48:20Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-08-21T06:25:48Z day: '05' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:12891 ec_funded: 1 file: - access_level: closed checksum: 59b0303dc483f40a96a610a90aab7ee9 content_type: application/pdf creator: aschauer date_created: 2023-05-05T13:01:14Z date_updated: 2023-05-05T13:01:14Z embargo: 2024-05-05 embargo_to: open_access file_id: '12907' file_name: Thesis_Schauer_final.pdf file_size: 31434230 relation: main_file - access_level: closed checksum: 25f54e12479b6adaabd129a20568e6c1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: aschauer date_created: 2023-05-05T13:04:15Z date_updated: 2023-05-05T13:04:15Z file_id: '12908' file_name: Thesis_Schauer_final.docx file_size: 43809109 relation: source_file file_date_updated: 2023-05-05T13:04:15Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '190' project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 26B1E39C-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8966' relation: part_of_dissertation status: public - id: '7888' relation: part_of_dissertation status: public status: public supervisor: - 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 title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12897' abstract: - lang: eng text: "Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner citation: ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897' apa: 'Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897' chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.' ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.' ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.' mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.' short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-05T10:40:14Z date_published: 2023-05-05T00:00:00Z date_updated: 2024-01-29T10:47:51Z day: '05' ddc: - '516' - '004' - '518' - '531' degree_awarded: PhD department: - _id: GradSch - _id: BeBi doi: 10.15479/at:ista:12897 ec_funded: 1 file: - access_level: open_access checksum: cc2094e92fa27000b70eb4bfb76d6b5a content_type: application/pdf creator: chafner date_created: 2023-05-11T10:43:20Z date_updated: 2023-12-08T23:30:04Z embargo: 2023-12-07 file_id: '12942' file_name: thesis-hafner-2023may11-a2b.pdf file_size: 50714445 relation: main_file - access_level: closed checksum: a6b51334be2b81672357b1549afab40c content_type: application/pdf creator: chafner date_created: 2023-05-11T10:43:44Z date_updated: 2023-12-08T23:30:04Z embargo_to: open_access file_id: '12943' file_name: thesis-release-form.pdf file_size: 265319 relation: source_file file_date_updated: 2023-12-08T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '180' project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: isbn: - 978-3-99078-031-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9817' relation: part_of_dissertation status: public - id: '7117' relation: part_of_dissertation status: public - id: '13188' relation: dissertation_contains status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models' type: dissertation user_id: 400429CC-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12900' abstract: - lang: eng text: "About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. " acknowledged_ssus: - _id: M-Shop - _id: SSU - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 citation: ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900 apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900 chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900. ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023. ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria. mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12900. short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023. date_created: 2023-05-05T11:08:50Z date_published: 2023-05-05T00:00:00Z date_updated: 2024-10-29T09:11:05Z day: '05' ddc: - '537' - '535' - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:12900 ec_funded: 1 file: - access_level: closed checksum: 8cbdab9c37ee55e591092a6f66b272c4 content_type: application/x-zip-compressed creator: rsahu date_created: 2023-05-09T08:45:14Z date_updated: 2023-06-06T22:30:03Z embargo_to: open_access file_id: '12928' file_name: thesis.zip file_size: 36767177 relation: source_file - access_level: closed checksum: 439659ead46618147309be39d9dd5a8c content_type: application/pdf creator: rsahu date_created: 2023-05-09T08:51:17Z date_updated: 2023-07-06T11:37:40Z file_id: '12929' file_name: thesis_pdfa_final.pdf file_size: 17501990 relation: main_file file_date_updated: 2023-07-06T11:37:40Z has_accepted_license: '1' keyword: - quantum optics - electrooptics - quantum networks - quantum communication - transduction language: - iso: eng month: '05' oa_version: Published Version page: '190' project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: isbn: - 978-3-99078-030-5 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9114' relation: part_of_dissertation status: public - id: '10924' relation: part_of_dissertation status: public - id: '13175' relation: new_edition status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Cavity quantum electrooptics 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: '2023' ... --- _id: '12933' abstract: - lang: eng text: Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster". article_processing_charge: No author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 citation: ama: 'Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933' apa: 'Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933' chicago: 'Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.' ieee: 'G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.' ista: 'Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.' mla: 'Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.' short: G. Puixeu Sala, (2023). contributor: - first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2023-05-10T10:00:49Z date_published: 2023-05-15T00:00:00Z date_updated: 2023-12-13T12:15:36Z day: '15' ddc: - '570' department: - _id: GradSch - _id: NiBa - _id: BeVi doi: 10.15479/AT:ISTA:12933 file: - access_level: open_access checksum: 0ba0bcd0bb8b18d84792136a4370df90 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:43Z date_updated: 2023-05-10T09:41:43Z file_id: '12934' file_name: Dataset_S1.csv file_size: 8029982 relation: main_file success: 1 - access_level: open_access checksum: a62aa9a6d4904e0fdb699cf752640863 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:43Z date_updated: 2023-05-10T09:41:43Z file_id: '12935' file_name: Dataset_S2.csv file_size: 13667640 relation: main_file success: 1 - access_level: open_access checksum: e20ea7f4f8a9bdf1b3849a44664ae58b content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:48Z date_updated: 2023-05-10T09:41:48Z file_id: '12936' file_name: Dataset_S3.csv file_size: 8369141 relation: main_file success: 1 - access_level: open_access checksum: f6156e5fc44446c907ddd0d7289d4cf8 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:50Z date_updated: 2023-05-10T09:41:50Z file_id: '12937' file_name: Dataset_S4.csv file_size: 19543247 relation: main_file success: 1 - access_level: open_access checksum: ae9f54c77a1c42b666ae6c1dfd33ac86 content_type: text/plain creator: gpuixeus date_created: 2023-05-11T12:50:18Z date_updated: 2023-05-11T12:50:18Z file_id: '12944' file_name: readme.txt file_size: 4566 relation: main_file success: 1 file_date_updated: 2023-05-11T12:50:18Z has_accepted_license: '1' month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14058' relation: used_in_publication status: public - id: '14077' relation: used_in_publication status: public status: public title: 'Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12964' abstract: - lang: eng text: "Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel R full_name: Boocock, Daniel R id: 453AF628-F248-11E8-B48F-1D18A9856A87 last_name: Boocock orcid: 0000-0002-1585-2631 citation: ama: Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964 apa: Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964 chicago: Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964. ieee: D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023. ista: Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. mla: Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964. short: D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023. date_created: 2023-05-15T14:52:36Z date_published: 2023-05-17T00:00:00Z date_updated: 2023-08-04T11:02:40Z day: '17' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: EdHa doi: 10.15479/at:ista:12964 ec_funded: 1 file: - access_level: closed checksum: d51240675fc6dc0e3f5dc0c902695d3a content_type: application/pdf creator: dboocock date_created: 2023-05-17T13:39:54Z date_updated: 2023-05-19T07:04:25Z embargo: 2024-05-17 embargo_to: open_access file_id: '12988' file_name: thesis_boocock.pdf file_size: 40414730 relation: main_file - access_level: closed checksum: 581a2313ffeb40fe77e8a122a25a7795 content_type: application/zip creator: dboocock date_created: 2023-05-17T13:39:53Z date_updated: 2023-05-17T14:35:13Z file_id: '12989' file_name: thesis_boocock.zip file_size: 34338567 relation: source_file file_date_updated: 2023-05-19T07:04:25Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '146' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-032-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8602' relation: part_of_dissertation status: public status: public supervisor: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Mechanochemical pattern formation across biological scales 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: '2023' ...