--- OA_place: publisher _id: '10429' abstract: - lang: eng text: "The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze orcid: 0000-0001-5634-0731 citation: ama: Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429 apa: Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429 chicago: Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429. ieee: G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021. ista: Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria. mla: Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429. short: G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-12-08T21:52:28Z date_published: 2021-12-09T00:00:00Z date_updated: 2026-04-08T07:00:46Z day: '09' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/at:ista:10429 ec_funded: 1 file: - access_level: open_access checksum: 6bf14e9a523387328f016c0689f5e10e content_type: application/pdf creator: gnadirad date_created: 2021-12-09T17:47:49Z date_updated: 2021-12-09T17:47:49Z file_id: '10436' file_name: Thesis_Final_09_12_2021.pdf file_size: 2370859 relation: main_file success: 1 - access_level: closed checksum: 914d6c5ca86bd0add471971a8f4c4341 content_type: application/zip creator: gnadirad date_created: 2021-12-09T17:47:49Z date_updated: 2022-03-28T12:55:12Z file_id: '10437' file_name: Thesis_Final_09_12_2021.zip file_size: 2596924 relation: source_file file_date_updated: 2022-03-28T12:55:12Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '132' project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10435' relation: part_of_dissertation status: public - id: '10432' relation: part_of_dissertation status: public - id: '6673' relation: part_of_dissertation status: public - id: '5965' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: On achieving scalability through relaxation type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9418' abstract: - lang: eng text: "Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models." acknowledged_ssus: - _id: ScienComp - _id: CampIT - _id: E-Lib alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai citation: ama: Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418 apa: Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418 chicago: Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418. ieee: M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021. ista: Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria. mla: Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418. short: M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-05-24T13:06:23Z date_published: 2021-05-30T00:00:00Z date_updated: 2026-04-08T07:01:17Z day: '30' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/AT:ISTA:9418 file: - access_level: open_access checksum: 4f0abe64114cfed264f9d36e8d1197e3 content_type: application/pdf creator: bphuong date_created: 2021-05-24T11:22:29Z date_updated: 2021-05-24T11:22:29Z file_id: '9419' file_name: mph-thesis-v519-pdfimages.pdf file_size: 2673905 relation: main_file success: 1 - access_level: closed checksum: f5699e876bc770a9b0df8345a77720a2 content_type: application/zip creator: bphuong date_created: 2021-05-24T11:56:02Z date_updated: 2021-05-24T11:56:02Z file_id: '9420' file_name: thesis.zip file_size: 92995100 relation: source_file file_date_updated: 2021-05-24T11:56:02Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '125' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7435' relation: part_of_dissertation status: deleted - id: '7481' relation: part_of_dissertation status: public - id: '9416' relation: part_of_dissertation status: public - id: '7479' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Underspecification in deep learning type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9056' abstract: - lang: eng text: "In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 citation: ama: Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:10.15479/AT:ISTA:9056 apa: Osang, G. F. (2021). Multi-cover persistence and Delaunay mosaics. Institute of Science and Technology Austria, Klosterneuburg. https://doi.org/10.15479/AT:ISTA:9056 chicago: Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9056. ieee: G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021. ista: 'Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.' mla: Osang, Georg F. Multi-Cover Persistence and Delaunay Mosaics. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9056. short: G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-02-02T14:11:06Z date_published: 2021-02-01T00:00:00Z date_updated: 2026-04-08T07:01:30Z day: '01' ddc: - '006' - '514' - '516' degree_awarded: PhD department: - _id: HeEd - _id: GradSch doi: 10.15479/AT:ISTA:9056 file: - access_level: closed checksum: bcf27986147cab0533b6abadd74e7629 content_type: application/zip creator: patrickd date_created: 2021-02-02T14:09:25Z date_updated: 2021-02-03T10:37:28Z file_id: '9063' file_name: thesis_source.zip file_size: 13446994 relation: source_file - access_level: open_access checksum: 9cc8af266579a464385bbe2aff6af606 content_type: application/pdf creator: patrickd date_created: 2021-02-02T14:09:18Z date_updated: 2021-02-02T14:09:18Z file_id: '9064' file_name: thesis_pdfA2b.pdf file_size: 5210329 relation: main_file success: 1 file_date_updated: 2021-02-03T10:37:28Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '02' oa: 1 oa_version: Published Version page: '134' place: Klosterneuburg publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '187' relation: part_of_dissertation status: public - id: '8703' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Multi-cover persistence and Delaunay mosaics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9920' abstract: - lang: eng text: 'This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.' acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 citation: ama: Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:10.15479/at:ista:9920 apa: Peruzzo, M. (2021). Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9920 chicago: Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9920. ieee: M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021. ista: Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria. mla: Peruzzo, Matilda. Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9920. short: M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-08-16T09:44:09Z date_published: 2021-08-19T00:00:00Z date_updated: 2026-04-15T06:43:02Z day: '19' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:9920 file: - access_level: closed checksum: 3cd1986efde5121d7581f6fcf9090da8 content_type: application/x-zip-compressed creator: mperuzzo date_created: 2021-08-16T09:33:21Z date_updated: 2021-09-06T08:39:47Z file_id: '9924' file_name: GeometricSuperinductorsForCQED.zip file_size: 151387283 relation: source_file - access_level: open_access checksum: 50928c621cdf0775d7a5906b9dc8602c content_type: application/pdf creator: mperuzzo date_created: 2021-08-18T14:20:06Z date_updated: 2021-09-06T08:39:47Z file_id: '9939' file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf file_size: 17596344 relation: main_file - access_level: closed checksum: 37f486aa1b622fe44af00d627ec13f6c content_type: application/pdf creator: mperuzzo date_created: 2021-08-18T14:20:09Z date_updated: 2021-09-06T08:39:47Z description: Extra copy of the thesis as PDF/A-2b file_id: '9940' file_name: GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf file_size: 17592425 relation: other file_date_updated: 2021-09-06T08:39:47Z has_accepted_license: '1' keyword: - quantum computing - superinductor - quantum metrology language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '149' publication_identifier: isbn: - 978-3-99078-013-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9928' relation: part_of_dissertation status: public - id: '8755' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Geometric superinductors and their applications in circuit quantum electrodynamics type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10035' abstract: - lang: eng text: 'Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for "graph-building" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).' acknowledgement: "I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein citation: ama: Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035 apa: Klein, K. (2021). On the adaptive security of graph-based games. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035 chicago: Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035. ieee: K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021. ista: Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria. mla: Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035. short: K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-09-23T07:31:44Z date_published: 2021-09-23T00:00:00Z date_updated: 2026-04-16T09:52:03Z day: '23' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/at:ista:10035 ec_funded: 1 file: - access_level: open_access checksum: 73a44345c683e81f3e765efbf86fdcc5 content_type: application/pdf creator: cchlebak date_created: 2021-10-04T12:22:33Z date_updated: 2021-10-04T12:22:33Z file_id: '10082' file_name: thesis_pdfa.pdf file_size: 2104726 relation: main_file success: 1 - access_level: closed checksum: 7b80df30a0e686c3ef6a56d4e1c59e29 content_type: application/x-zip-compressed creator: cchlebak date_created: 2021-10-05T07:04:37Z date_updated: 2022-03-10T12:15:18Z file_id: '10085' file_name: thesis_final (1).zip file_size: 9538359 relation: source_file file_date_updated: 2022-03-10T12:15:18Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '276' project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10044' relation: part_of_dissertation status: public - id: '10048' relation: part_of_dissertation status: public - id: '10041' relation: part_of_dissertation status: public - id: '10049' relation: part_of_dissertation status: public - id: '637' relation: part_of_dissertation status: public - id: '6430' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: On the adaptive security of graph-based games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10293' abstract: - lang: eng text: "Indirect reciprocity in evolutionary game theory is a prominent mechanism for explaining the evolution of cooperation among unrelated individuals. In contrast to direct reciprocity, which is based on individuals meeting repeatedly, and conditionally cooperating by using their own experiences, indirect reciprocity is based on individuals’ reputations. If a player helps another, this increases the helper’s public standing, benefitting them in the future. This lets cooperation in the population emerge without individuals having to meet more than once. While the two modes of reciprocity are intertwined, they are difficult to compare. Thus, they are usually studied in isolation. Direct reciprocity can maintain cooperation with simple strategies, and is robust against noise even when players do not remember more\r\nthan their partner’s last action. Meanwhile, indirect reciprocity requires its successful strategies, or social norms, to be more complex. Exhaustive search previously identified eight such norms, called the “leading eight”, which excel at maintaining cooperation. However, as the first result of this thesis, we show that the leading eight break down once we remove the fundamental assumption that information is synchronized and public, such that everyone agrees on reputations. Once we consider a more realistic scenario of imperfect information, where reputations are private, and individuals occasionally misinterpret or miss observations, the leading eight do not promote cooperation anymore. Instead, minor initial disagreements can proliferate, fragmenting populations into subgroups. In a next step, we consider ways to mitigate this issue. We first explore whether introducing “generosity” can stabilize cooperation when players use the leading eight strategies in noisy environments. This approach of modifying strategies to include probabilistic elements for coping with errors is known to work well in direct reciprocity. However, as we show here, it fails for the more complex norms of indirect reciprocity. Imperfect information still prevents cooperation from evolving. On the other hand, we succeeded to show in this thesis that modifying the leading eight to use “quantitative assessment”, i.e. tracking reputation scores on a scale beyond good and bad, and making overall judgments of others based on a threshold, is highly successful, even when noise increases in the environment. Cooperation can flourish when reputations\r\nare more nuanced, and players have a broader understanding what it means to be “good.” Finally, we present a single theoretical framework that unites the two modes of reciprocity despite their differences. Within this framework, we identify a novel simple and successful strategy for indirect reciprocity, which can cope with noisy environments and has an analogue in direct reciprocity. We can also analyze decision making when different sources of information are available. Our results help highlight that for sustaining cooperation, already the most simple rules of reciprocity can be sufficient." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 citation: ama: Schmid L. Evolution of cooperation via (in)direct reciprocity under imperfect information. 2021. doi:10.15479/at:ista:10293 apa: Schmid, L. (2021). Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10293 chicago: Schmid, Laura. “Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10293. ieee: L. Schmid, “Evolution of cooperation via (in)direct reciprocity under imperfect information,” Institute of Science and Technology Austria, 2021. ista: Schmid L. 2021. Evolution of cooperation via (in)direct reciprocity under imperfect information. Institute of Science and Technology Austria. mla: Schmid, Laura. Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10293. short: L. Schmid, Evolution of Cooperation via (in)Direct Reciprocity under Imperfect Information, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-11-15T17:12:57Z date_published: 2021-11-17T00:00:00Z date_updated: 2026-04-08T07:11:20Z day: '17' ddc: - '519' - '576' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/at:ista:10293 ec_funded: 1 file: - access_level: closed checksum: 86a05b430756ca12ae8107b6e6f3c1e5 content_type: application/zip creator: lschmid date_created: 2021-11-18T12:41:46Z date_updated: 2022-12-20T23:30:08Z embargo_to: open_access file_id: '10305' file_name: submission_new.zip file_size: 29703124 relation: source_file - access_level: open_access checksum: d940af042e94660c6b6a7b4f0b184d47 content_type: application/pdf creator: lschmid date_created: 2021-11-18T12:59:15Z date_updated: 2022-12-20T23:30:08Z embargo: 2022-10-18 file_id: '10306' file_name: thesis_new_upload.pdf file_size: 8320985 relation: main_file file_date_updated: 2022-12-20T23:30:08Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '171' project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9997' relation: part_of_dissertation status: public - id: '9402' relation: part_of_dissertation status: public - id: '2' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Evolution of cooperation via (in)direct reciprocity under imperfect information type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9992' abstract: - lang: eng text: "Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. " acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 citation: ama: Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:10.15479/at:ista:9992 apa: Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992 chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992. ieee: L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021. ista: Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria. mla: Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992. short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-09-09T07:37:20Z date_published: 2021-09-13T00:00:00Z date_updated: 2026-04-08T07:11:47Z day: '13' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:9992 ec_funded: 1 file: - access_level: closed checksum: c763064adaa720e16066c1a4f9682bbb content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lhoermaye date_created: 2021-09-09T07:29:48Z date_updated: 2021-09-15T22:30:26Z embargo_to: open_access file_id: '9993' file_name: Thesis_vupload.docx file_size: 25179004 relation: source_file - access_level: open_access checksum: 53911b06e93d7cdbbf4c7f4c162fa70f content_type: application/pdf creator: lhoermaye date_created: 2021-09-09T14:25:08Z date_updated: 2021-09-15T22:30:26Z embargo: 2021-09-09 file_id: '9996' file_name: Thesis_vfinal_pdfa.pdf file_size: 6246900 relation: main_file file_date_updated: 2021-09-15T22:30:26Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version page: '168' project: - _id: 262EF96E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29988 name: RNA-directed DNA methylation in plant development - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6943' relation: part_of_dissertation status: public - id: '8002' relation: part_of_dissertation status: public - id: '6351' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Wound healing in the Arabidopsis root meristem tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10135' abstract: - lang: eng text: "Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and\r\ncytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and\r\ntranslation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using\r\nchemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to\r\ncytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hana full_name: Semerádová, Hana id: 42FE702E-F248-11E8-B48F-1D18A9856A87 last_name: Semerádová citation: ama: Semerádová H. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. 2021. doi:10.15479/at:ista:10135 apa: Semerádová, H. (2021). Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10135 chicago: Semerádová, Hana. “Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10135. ieee: H. Semerádová, “Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis,” Institute of Science and Technology Austria, 2021. ista: Semerádová H. 2021. Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis. Institute of Science and Technology Austria. mla: Semerádová, Hana. Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10135. short: H. Semerádová, Molecular Mechanisms of the Cytokinin-Regulated Endomembrane Trafficking to Coordinate Plant Organogenesis, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-10-13T13:42:48Z date_published: 2021-10-13T00:00:00Z date_updated: 2026-04-08T07:12:06Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10135 file: - access_level: closed checksum: ce7108853e6cec6224f17cd6429b51fe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cziletti date_created: 2021-10-27T07:45:37Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10186' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3.docx file_size: 28508629 relation: source_file - access_level: open_access checksum: 0d7afb846e8e31ec794de47bf44e12ef content_type: application/pdf creator: cziletti date_created: 2021-10-27T07:45:57Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-10-28 file_id: '10187' file_name: Hana_Semeradova_Disertation_Thesis_II_Revised_3PDFA.pdf file_size: 10623525 relation: main_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 261821BC-B435-11E9-9278-68D0E5697425 grant_number: '24746' name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis publication_identifier: isbn: - 978-3-99078-014-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10058' abstract: - lang: eng text: 'Quantum information and computation has become a vast field paved with opportunities for researchers and investors. As large multinational companies and international funds are heavily investing in quantum technologies it is still a question which platform is best suited for the task of realizing a scalable quantum processor. In this work we investigate hole spins in Ge quantum wells. These hold great promise as they possess several favorable properties: a small effective mass, a strong spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine noise. All these characteristics helped Ge hole spin qubits to evolve from a single qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated a qubit approach leveraging the large out-of-plane g-factors of heavy hole states in Ge quantum dots. We found this qubit to be reproducibly operable at extremely low magnetic field and at large speeds while maintaining coherence. This was possible because large differences of g-factors in adjacent dots can be achieved in the out-of-plane direction. In the in-plane direction the small g-factors, on the other hand, can be altered very effectively by the confinement potentials. Here, we found that this can even lead to a sign change of the g-factors. The resulting g-factor difference alters the dynamics of the system drastically and produces effects typically attributed to a spin-orbit induced spin-flip term. The investigations carried out in this thesis give further insights into the possibilities of holes in Ge and reveal new physical properties that need to be considered when designing future spin qubit experiments.' acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No P30207, and the Nomis foundation. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 citation: ama: Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. 2021. doi:10.15479/at:ista:10058 apa: Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10058 chicago: Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10058. ieee: D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases,” Institute of Science and Technology Austria, 2021. ista: Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases. Institute of Science and Technology Austria. mla: Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058. short: D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional Ge Hole Gases, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-09-30T07:53:49Z date_published: 2021-10-05T00:00:00Z date_updated: 2026-04-08T07:12:19Z day: '05' ddc: - '621' - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:10058 file: - access_level: closed checksum: ad6bcb24083ed7c02baaf1885c9ea3d5 content_type: application/x-zip-compressed creator: djirovec date_created: 2021-09-30T14:29:14Z date_updated: 2022-12-20T23:30:07Z embargo_to: open_access file_id: '10061' file_name: PHD_Thesis_Jirovec_Source.zip file_size: 32397600 relation: source_file - access_level: open_access checksum: 5fbe08d4f66d1153e04c47971538fae8 content_type: application/pdf creator: djirovec date_created: 2021-10-05T07:56:49Z date_updated: 2022-12-20T23:30:07Z embargo: 2022-10-06 file_id: '10087' file_name: PHD_Thesis_pdfa2b_1.pdf file_size: 26910829 relation: main_file file_date_updated: 2022-12-20T23:30:07Z has_accepted_license: '1' keyword: - qubits - quantum computing - holes language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '151' project: - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10066' relation: part_of_dissertation status: public - id: '10065' relation: part_of_dissertation status: public - id: '8831' relation: part_of_dissertation status: public - id: '8909' relation: part_of_dissertation status: public - id: '5816' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole gases tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9562' abstract: - lang: eng text: Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry. acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: David full_name: Kleindienst, David id: 42E121A4-F248-11E8-B48F-1D18A9856A87 last_name: Kleindienst citation: ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:10.15479/at:ista:9562' apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562' chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.' ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.' ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.' mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.' short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.' corr_author: '1' date_created: 2021-06-17T14:10:47Z date_published: 2021-06-01T00:00:00Z date_updated: 2026-04-08T07:12:31Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:9562 file: - access_level: open_access checksum: 659df5518db495f679cb1df9e9bd1d94 content_type: application/pdf creator: dkleindienst date_created: 2021-06-17T14:03:14Z date_updated: 2022-07-02T22:30:04Z embargo: 2022-07-01 file_id: '9563' file_name: Thesis.pdf file_size: 77299142 relation: main_file - access_level: closed checksum: 3bcf63a2b19e5b6663be051bea332748 content_type: application/zip creator: dkleindienst date_created: 2021-06-17T14:04:30Z date_updated: 2022-07-02T22:30:04Z embargo_to: open_access file_id: '9564' file_name: Thesis_source.zip file_size: 369804895 relation: source_file file_date_updated: 2022-07-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '124' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9756' relation: part_of_dissertation status: public - id: '9437' relation: part_of_dissertation status: public - id: '612' relation: part_of_dissertation status: public - id: '8532' relation: part_of_dissertation status: public 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: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9397' abstract: - lang: eng text: Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karla full_name: Huljev, Karla id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87 last_name: Huljev citation: ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397 apa: Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397 chicago: Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397. ieee: K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021. ista: Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria. mla: Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397. short: K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-05-17T12:31:30Z date_published: 2021-05-18T00:00:00Z date_updated: 2026-04-08T07:12:51Z day: '18' ddc: - '571' degree_awarded: PhD department: - _id: CaHe - _id: GradSch doi: 10.15479/at:ista:9397 file: - access_level: closed checksum: 7f98532f5324a0b2f3fa8de2967baa19 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: khuljev date_created: 2021-05-17T12:29:12Z date_updated: 2022-05-21T22:30:04Z embargo_to: open_access file_id: '9398' file_name: KHuljev_Thesis_corrections.docx file_size: 47799741 relation: source_file - access_level: open_access checksum: bf512f8a1e572a543778fc4b227c01ba content_type: application/pdf creator: khuljev date_created: 2021-05-18T14:50:28Z date_updated: 2022-05-21T22:30:04Z embargo: 2022-05-20 file_id: '9401' file_name: new_KHuljev_Thesis_corrections.pdf file_size: 16542131 relation: main_file file_date_updated: 2022-05-21T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '101' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria 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: Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10307' abstract: - lang: eng text: Bacteria-host interactions represent a continuous trade-off between benefit and risk. Thus, the host immune response is faced with a non-trivial problem – accommodate beneficial commensals and remove harmful pathogens. This is especially difficult as molecular patterns, such as lipopolysaccharide or specific surface organelles such as pili, are conserved in both, commensal and pathogenic bacteria. Type 1 pili, tightly regulated by phase variation, are considered an important virulence factor of pathogenic bacteria as they facilitate invasion into host cells. While invasion represents a de facto passive mechanism for pathogens to escape the host immune response, we demonstrate a fundamental role of type 1 pili as active modulators of the innate and adaptive immune response. acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: PreCl - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X citation: ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021. doi:10.15479/at:ista:10307 apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307 chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307. ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,” Institute of Science and Technology Austria, 2021. ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response. Institute of Science and Technology Austria. mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307. short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-11-18T15:05:06Z date_published: 2021-11-18T00:00:00Z date_updated: 2026-04-08T07:14:01Z day: '18' ddc: - '570' degree_awarded: PhD department: - _id: MiSi - _id: CaGu - _id: GradSch doi: 10.15479/at:ista:10307 file: - access_level: open_access checksum: b39c9e0ef18d0484d537a67551effd02 content_type: application/pdf creator: ktomasek date_created: 2021-11-18T15:07:31Z date_updated: 2022-12-20T23:30:05Z embargo: 2022-11-18 file_id: '10308' file_name: ThesisTomasekKathrin.pdf file_size: 13266088 relation: main_file - access_level: closed checksum: c0c440ee9e5ef1102a518a4f9f023e7c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ktomasek date_created: 2021-11-18T15:07:46Z date_updated: 2022-12-20T23:30:05Z embargo_to: open_access file_id: '10309' file_name: ThesisTomasekKathrin.docx file_size: 7539509 relation: source_file file_date_updated: 2022-12-20T23:30:05Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '73' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10316' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Pathogenic Escherichia coli hijack the host immune response type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9962' abstract: - lang: eng text: The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen citation: ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:10.15479/at:ista:9962 apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9962 chicago: Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9962. ieee: A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021. ista: Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria. mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9962. short: A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-08-29T12:36:50Z date_published: 2021-09-02T00:00:00Z date_updated: 2026-04-08T07:19:09Z day: '02' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/at:ista:9962 file: - access_level: closed checksum: 66b56f5b988b233dc66a4f4b4fb2cdfe content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ahansen date_created: 2021-08-30T09:17:39Z date_updated: 2022-09-03T22:30:04Z embargo_to: open_access file_id: '9971' file_name: Thesis_Hansen.docx file_size: 10629190 relation: source_file - access_level: open_access checksum: 204fa40321a1c6289b68c473634c4bf3 content_type: application/pdf creator: ahansen date_created: 2021-08-30T09:29:44Z date_updated: 2022-09-03T22:30:04Z embargo: 2022-09-02 file_id: '9972' file_name: Thesis_Hansen_PDFA-1a.pdf file_size: 13457469 relation: main_file file_date_updated: 2022-09-03T22:30:04Z has_accepted_license: '1' keyword: - Neuronal migration - Non-cell-autonomous - Cell-autonomous - Neurodevelopmental disease language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '182' project: - _id: 2625A13E-B435-11E9-9278-68D0E5697425 grant_number: '24812' name: Molecular mechanisms of radial neuronal migration publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8569' relation: part_of_dissertation status: public - id: '960' relation: part_of_dissertation status: public status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9623' abstract: - lang: eng text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n" acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Silvia full_name: Caballero Mancebo, Silvia id: 2F1E1758-F248-11E8-B48F-1D18A9856A87 last_name: Caballero Mancebo orcid: 0000-0002-5223-3346 citation: ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:10.15479/at:ista:9623 apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623 chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623. ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021. ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria. mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623. short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-07-01T14:50:17Z date_published: 2021-07-01T00:00:00Z date_updated: 2026-04-08T07:19:38Z ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:9623 file: - access_level: closed checksum: e039225a47ef32666d59bf35ddd30ecf content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: scaballe date_created: 2021-07-01T14:48:54Z date_updated: 2022-07-02T22:30:06Z embargo_to: open_access file_id: '9624' file_name: PhDThesis_SCM.docx file_size: 131946790 relation: source_file - access_level: open_access checksum: dd4d78962ea94ad95e97ca7d9af08f4b content_type: application/pdf creator: scaballe date_created: 2021-07-01T14:46:25Z date_updated: 2022-07-02T22:30:06Z embargo: 2022-07-01 file_id: '9625' file_name: PhDThesis_SCM.pdf file_size: 17094958 relation: main_file file_date_updated: 2022-07-02T22:30:06Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '111' publication_identifier: isbn: - 978-3-99078-012-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9750' relation: part_of_dissertation status: public - id: '9006' 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: Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10303' abstract: - lang: eng text: 'Nitrogen is an essential macronutrient determining plant growth, development and affecting agricultural productivity. Root, as a hub that perceives and integrates local and systemic signals on the plant’s external and endogenous nitrogen resources, communicates with other plant organs to consolidate their physiology and development in accordance with actual nitrogen balance. Over the last years, numerous studies demonstrated that these comprehensive developmental adaptations rely on the interaction between pathways controlling nitrogen homeostasis and hormonal networks acting globally in the plant body. However, molecular insights into how the information about the nitrogen status is translated through hormonal pathways into specific developmental output are lacking. In my work, I addressed so far poorly understood mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment of shoot growth and development after nitrate provision. Applying a combination of molecular, cell, and developmental biology approaches, genetics and grafting experiments as well as hormonal analytics, I identified and characterized an unknown molecular framework orchestrating shoot development with a root nitrate sensory system. ' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rashed full_name: Abualia, Rashed id: 4827E134-F248-11E8-B48F-1D18A9856A87 last_name: Abualia orcid: 0000-0002-9357-9415 citation: ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303 apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303 chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303. ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science and Technology Austria, 2021. ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of Science and Technology Austria. mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303. short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-11-18T11:20:59Z date_published: 2021-11-22T00:00:00Z date_updated: 2026-04-08T07:20:07Z day: '22' ddc: - '580' - '581' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/at:ista:10303 file: - access_level: open_access checksum: dea38b98aa4da1cea03dcd0f10862818 content_type: application/pdf creator: rabualia date_created: 2021-11-22T14:48:21Z date_updated: 2022-12-20T23:30:06Z embargo: 2022-11-23 file_id: '10331' file_name: AbualiaPhDthesisfinalv3.pdf file_size: 28005730 relation: main_file - access_level: closed checksum: 4cd62da5ec5ba4c32e61f0f6d9e61920 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rabualia date_created: 2021-11-22T14:48:34Z date_updated: 2022-12-20T23:30:06Z embargo_to: open_access file_id: '10332' file_name: AbualiaPhDthesisfinalv3.docx file_size: 62841883 relation: source_file file_date_updated: 2022-12-20T23:30:06Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '139' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '47' relation: part_of_dissertation status: public - id: '9913' relation: part_of_dissertation status: public - id: '9010' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Role of hormones in nitrate regulated growth tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '9728' abstract: - lang: eng text: "Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nishchal full_name: Agrawal, Nishchal id: 469E6004-F248-11E8-B48F-1D18A9856A87 last_name: Agrawal citation: ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:10.15479/at:ista:9728 apa: Agrawal, N. (2021). Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9728 chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9728. ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021. ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria. mla: Agrawal, Nishchal. Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9728. short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-07-27T13:40:30Z date_published: 2021-07-29T00:00:00Z date_updated: 2026-04-16T08:43:20Z day: '29' ddc: - '532' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:9728 file: - access_level: closed checksum: 77436be3563a90435024307b1b5ee7e8 content_type: application/x-zip-compressed creator: nagrawal date_created: 2021-07-28T13:32:02Z date_updated: 2022-07-29T22:30:05Z embargo_to: open_access file_id: '9744' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip file_size: 22859658 relation: source_file - access_level: open_access checksum: 72a891d7daba85445c29b868c22575ed content_type: application/pdf creator: nagrawal date_created: 2021-07-28T13:32:05Z date_updated: 2022-07-29T22:30:05Z embargo: 2022-07-28 file_id: '9745' file_name: Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf file_size: 18658048 relation: main_file file_date_updated: 2022-07-29T22:30:05Z has_accepted_license: '1' keyword: - Drag Reduction - Transition to Turbulence - Multiphase Flows - particle Laden Flows - Complex Flows - Experiments - Fluid Dynamics language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '118' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6189' relation: part_of_dissertation 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: Transition to turbulence and drag reduction in particle-laden pipe flows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '8934' abstract: - lang: eng text: "In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.\r\nWe use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades." acknowledgement: 'The research was partially supported by an IBM PhD fellowship, a Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences (OeAW).' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: Goharshady AK. Parameterized and algebro-geometric advances in static program analysis. 2021. doi:10.15479/AT:ISTA:8934 apa: Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934 chicago: Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances in Static Program Analysis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:8934. ieee: A. K. Goharshady, “Parameterized and algebro-geometric advances in static program analysis,” Institute of Science and Technology Austria, 2021. ista: Goharshady AK. 2021. Parameterized and algebro-geometric advances in static program analysis. Institute of Science and Technology Austria. mla: Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances in Static Program Analysis. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:8934. short: A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program Analysis, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2020-12-10T12:17:07Z date_published: 2021-01-01T00:00:00Z date_updated: 2026-04-16T10:07:18Z day: '01' ddc: - '005' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/AT:ISTA:8934 file: - access_level: open_access checksum: d1b9db3725aed34dadd81274aeb9426c content_type: application/pdf creator: akafshda date_created: 2020-12-22T20:08:44Z date_updated: 2021-12-23T23:30:04Z embargo: 2021-12-22 file_id: '8969' file_name: Thesis-pdfa.pdf file_size: 5251507 relation: main_file - access_level: closed checksum: 1661df7b393e6866d2460eba3c905130 content_type: application/zip creator: akafshda date_created: 2020-12-22T20:08:50Z date_updated: 2021-03-04T23:30:04Z embargo_to: open_access file_id: '8970' file_name: source.zip file_size: 10636756 relation: source_file file_date_updated: 2021-12-23T23:30:04Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/publicdomain/zero/1.0/ month: '01' oa: 1 oa_version: Published Version page: '278' project: - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6490' relation: part_of_dissertation status: public - id: '6780' relation: part_of_dissertation status: public - id: '7158' relation: part_of_dissertation status: public - id: '66' relation: part_of_dissertation status: public - id: '6378' relation: part_of_dissertation status: public - id: '311' relation: part_of_dissertation status: public - id: '6175' relation: part_of_dissertation status: public - id: '6340' relation: part_of_dissertation status: public - id: '7014' relation: part_of_dissertation status: public - id: '6009' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '8728' relation: part_of_dissertation status: public - id: '8089' relation: part_of_dissertation status: public - id: '6380' relation: part_of_dissertation status: public - id: '5977' relation: part_of_dissertation status: public - id: '6056' relation: part_of_dissertation status: public - id: '639' relation: part_of_dissertation status: public - id: '1386' relation: part_of_dissertation status: public - id: '6918' relation: part_of_dissertation status: public - id: '7810' relation: part_of_dissertation status: public - id: '949' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Parameterized and algebro-geometric advances in static program analysis 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '10083' abstract: - lang: eng text: "Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X citation: ama: Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:10.15479/at:ista:10083 apa: Li, L. (2021). Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10083 chicago: Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10083. ieee: L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021. ista: Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria. mla: Li, Lanxin. Rapid Cell Growth Regulation in Arabidopsis. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10083. short: L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-10-04T13:33:10Z date_published: 2021-10-06T00:00:00Z date_updated: 2026-04-16T12:20:41Z day: '06' ddc: - '575' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/at:ista:10083 ec_funded: 1 file: - access_level: open_access checksum: 3b2f55b3b8ae05337a0dcc1cd8595b10 content_type: application/pdf creator: cchlebak date_created: 2021-10-14T08:00:07Z date_updated: 2022-12-20T23:30:03Z embargo: 2022-10-14 file_id: '10138' file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf file_size: 8616142 relation: main_file - access_level: closed checksum: f23ed258ca894f6aabf58b0c128bf242 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2021-10-14T08:00:13Z date_updated: 2022-12-20T23:30:03Z embargo_to: open_access file_id: '10139' file_name: 0._IST_Austria_Thesis_Lanxin_Li_1014.docx file_size: 15058499 relation: source_file file_date_updated: 2022-12-20T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '442' relation: part_of_dissertation status: public - id: '6627' relation: part_of_dissertation status: public - id: '8931' relation: part_of_dissertation status: public - id: '8986' relation: part_of_dissertation status: public - id: '10095' relation: part_of_dissertation status: public - id: '8283' relation: part_of_dissertation status: public - id: '9287' relation: part_of_dissertation status: public - id: '10015' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Rapid cell growth regulation in Arabidopsis tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2021' ... --- OA_place: publisher _id: '7944' abstract: - lang: eng text: "This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 citation: ama: Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944 apa: Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944 chicago: Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944. ieee: Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020. ista: Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria. mla: Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944. short: Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-06-08T00:49:46Z date_published: 2020-06-09T00:00:00Z date_updated: 2026-04-08T07:23:01Z day: '09' ddc: - '516' - '514' degree_awarded: PhD department: - _id: HeEd - _id: UlWa doi: 10.15479/AT:ISTA:7944 file: - access_level: open_access checksum: df688bc5a82b50baee0b99d25fc7b7f0 content_type: application/pdf creator: zmasarov date_created: 2020-06-08T00:34:00Z date_updated: 2020-07-14T12:48:05Z file_id: '7945' file_name: THESIS_Zuzka_Masarova.pdf file_size: 13661779 relation: main_file - access_level: closed checksum: 45341a35b8f5529c74010b7af43ac188 content_type: application/zip creator: zmasarov date_created: 2020-06-08T00:35:30Z date_updated: 2020-07-14T12:48:05Z file_id: '7946' file_name: THESIS_Zuzka_Masarova_SOURCE_FILES.zip file_size: 32184006 relation: source_file file_date_updated: 2020-07-14T12:48:05Z has_accepted_license: '1' keyword: - reconfiguration - reconfiguration graph - triangulations - flip - constrained triangulations - shellability - piecewise-linear balls - token swapping - trees - coloured weighted token swapping language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '06' oa: 1 oa_version: Published Version page: '160' publication_identifier: isbn: - 978-3-99078-005-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7950' relation: part_of_dissertation status: public - id: '5986' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Reconfiguration problems tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- OA_place: publisher _id: '7629' abstract: - lang: eng text: "This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dominik L full_name: Forkert, Dominik L id: 35C79D68-F248-11E8-B48F-1D18A9856A87 last_name: Forkert citation: ama: Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629 apa: Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629 chicago: Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629. ieee: D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020. ista: Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. mla: Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629. short: D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-04-02T06:40:23Z date_published: 2020-03-31T00:00:00Z date_updated: 2026-04-08T07:22:00Z day: '31' ddc: - '510' degree_awarded: PhD department: - _id: JaMa doi: 10.15479/AT:ISTA:7629 ec_funded: 1 file: - access_level: open_access checksum: c814a1a6195269ca6fe48b0dca45ae8a content_type: application/pdf creator: dernst date_created: 2020-04-14T10:47:59Z date_updated: 2020-07-14T12:48:01Z file_id: '7657' file_name: Thesis_Forkert_PDFA.pdf file_size: 3297129 relation: main_file - access_level: closed checksum: ceafb53f923d1b5bdf14b2b0f22e4a81 content_type: application/x-zip-compressed creator: dernst date_created: 2020-04-14T10:47:59Z date_updated: 2020-07-14T12:48:01Z file_id: '7658' file_name: Thesis_Forkert_source.zip file_size: 1063908 relation: source_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '154' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ...