--- _id: '14547' abstract: - lang: eng text: "Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier." acknowledged_ssus: - _id: NanoFab - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan citation: ama: Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547 apa: Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547 chicago: Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547. ieee: D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023. ista: Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. mla: Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547. short: D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023. date_created: 2023-11-17T13:45:26Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-11-30T10:56:04Z day: '16' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/14547 file: - access_level: open_access checksum: db0c37d213bc002125bd59690e9db246 content_type: application/pdf creator: pduc date_created: 2023-11-17T13:36:44Z date_updated: 2023-11-22T09:46:06Z file_id: '14548' file_name: Phan_Thesis_pdfa.pdf file_size: 34828019 relation: main_file - access_level: closed checksum: 8d3bd6afa279a0078ffd13e06bb6d56d content_type: application/zip creator: pduc date_created: 2023-11-17T13:44:53Z date_updated: 2023-11-17T13:47:54Z file_id: '14549' file_name: dissertation_src.zip file_size: 279319709 relation: source_file file_date_updated: 2023-11-22T09:46:06Z has_accepted_license: '1' keyword: - superconductor-semiconductor - superconductivity - Al - InAs - p-wave - superconductivity - JPA - microwave language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '80' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10851' relation: part_of_dissertation status: public - id: '13264' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Resonant microwave spectroscopy of Al-InAs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14587' abstract: - lang: eng text: "This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero." acknowledgement: The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alice full_name: Marveggio, Alice id: 25647992-AA84-11E9-9D75-8427E6697425 last_name: Marveggio citation: ama: Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587 apa: Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587 chicago: Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587. ieee: A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023. ista: Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. mla: Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587. short: A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023. date_created: 2023-11-21T11:41:05Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-11-30T13:25:03Z day: '21' ddc: - '515' degree_awarded: PhD department: - _id: GradSch - _id: JuFi doi: 10.15479/at:ista:14587 ec_funded: 1 file: - access_level: open_access checksum: 6c7db4cc86da6cdc79f7f358dc7755d4 content_type: application/pdf creator: amarvegg date_created: 2023-11-29T09:09:31Z date_updated: 2023-11-29T09:09:31Z file_id: '14626' file_name: thesis_Marveggio.pdf file_size: 2881100 relation: main_file success: 1 - access_level: open_access checksum: 52f28bdf95ec82cff39f3685f9c48e7d content_type: application/zip creator: amarvegg date_created: 2023-11-29T09:10:19Z date_updated: 2023-11-29T09:28:30Z file_id: '14627' file_name: Thesis_Marveggio.zip file_size: 10189696 relation: source_file file_date_updated: 2023-11-29T09:28:30Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '228' project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11842' relation: part_of_dissertation status: public - id: '14597' relation: part_of_dissertation status: public status: public supervisor: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X title: Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14622' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefan full_name: Sack, Stefan id: dd622248-f6e0-11ea-865d-ce382a1c81a5 last_name: Sack orcid: 0000-0001-5400-8508 citation: ama: 'Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622' apa: 'Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622' chicago: 'Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.' ieee: 'S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.' ista: 'Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.' mla: 'Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.' short: 'S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.' date_created: 2023-11-28T10:58:13Z date_published: 2023-11-30T00:00:00Z date_updated: 2023-12-13T14:47:25Z day: '30' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:14622 ec_funded: 1 file: - access_level: closed checksum: 068fd3570506ec42b2faa390de784bc4 content_type: application/pdf creator: ssack date_created: 2023-11-30T15:53:10Z date_updated: 2023-12-01T11:10:46Z embargo: 2024-11-30 embargo_to: open_access file_id: '14635' file_name: PhD_Thesis.pdf file_size: 11947523 relation: main_file - access_level: closed checksum: 0fa3bc0d108aed0ac59d2c6beef2220a content_type: application/zip creator: ssack date_created: 2023-11-30T15:54:11Z date_updated: 2023-12-01T11:10:46Z file_id: '14636' file_name: PhD Thesis (1).zip file_size: 18422964 relation: source_file file_date_updated: 2023-12-01T11:10:46Z has_accepted_license: '1' language: - iso: eng month: '11' oa_version: Published Version page: '142' project: - _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d name: Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11471' relation: part_of_dissertation status: public - id: '13125' relation: part_of_dissertation status: public - id: '9760' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: 'Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14628' abstract: - lang: eng text: We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration. acknowledgement: "The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program." article_number: '168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Liane full_name: Makatura, Liane last_name: Makatura - first_name: Bohan full_name: Wang, Bohan last_name: Wang - first_name: Yi-Lu full_name: Chen, Yi-Lu id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70 last_name: Chen - first_name: Bolei full_name: Deng, Bolei last_name: Deng - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik citation: ama: 'Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389' apa: 'Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., & Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3605389' chicago: 'Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.' ieee: 'L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.' ista: 'Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.' mla: 'Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389.' short: L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023). date_created: 2023-11-29T15:02:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2023-12-04T08:09:05Z day: '01' ddc: - '531' - '006' department: - _id: GradSch - _id: ChWo - _id: BeBi doi: 10.1145/3605389 file: - access_level: open_access checksum: 0192f597d7a2ceaf89baddfd6190d4c8 content_type: application/zip creator: yichen date_created: 2023-11-29T15:16:01Z date_updated: 2023-11-29T15:16:01Z file_id: '14630' file_name: tog-22-0089-File004.zip file_size: 95467870 relation: main_file success: 1 - access_level: open_access checksum: 7fb024963be81933494f38de191e4710 content_type: application/zip creator: yichen date_created: 2023-11-29T15:16:01Z date_updated: 2023-11-29T15:16:01Z file_id: '14631' file_name: tog-22-0089-File005.zip file_size: 103731880 relation: main_file success: 1 - access_level: open_access checksum: b7d6829ce396e21cac9fae0ec7130a6b content_type: application/pdf creator: dernst date_created: 2023-12-04T08:04:14Z date_updated: 2023-12-04T08:04:14Z file_id: '14638' file_name: 2023_ACMToG_Makatura.pdf file_size: 57067476 relation: main_file success: 1 file_date_updated: 2023-12-04T08:04:14Z has_accepted_license: '1' intvolume: ' 42' issue: '5' keyword: - Computer Graphics and Computer-Aided Design language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 - 1557-7368 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: 'Procedural metamaterials: A unified procedural graph for metamaterial design' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14641' acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mike full_name: Hennessey-Wesen, Mike id: 3F338C72-F248-11E8-B48F-1D18A9856A87 last_name: Hennessey-Wesen citation: ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641 apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641 chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641. ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023. ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641. short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023. date_created: 2023-12-04T13:17:37Z date_published: 2023-11-30T00:00:00Z date_updated: 2023-12-07T14:12:25Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:14641 ec_funded: 1 file: - access_level: closed checksum: 4127c285b34f4bf7fb31ef24f9d14c25 content_type: application/vnd.oasis.opendocument.text creator: mhenness date_created: 2023-12-06T13:13:26Z date_updated: 2023-12-06T13:13:26Z file_id: '14648' file_name: mike_thesis_v06-12-2023.odt file_size: 46405919 relation: source_file - access_level: closed checksum: f5203a61eddaf35235bbc51904d73982 content_type: application/pdf creator: mhenness date_created: 2023-12-06T13:14:15Z date_updated: 2023-12-06T13:14:15Z embargo: 2024-11-30 embargo_to: open_access file_id: '14649' file_name: mike_thesis_v06-12-2023.pdf file_size: 21282155 relation: main_file file_date_updated: 2023-12-06T13:14:15Z has_accepted_license: '1' keyword: - microfluidics - miceobiology - mutations - quorum sensing language: - iso: eng month: '11' oa_version: Published Version page: '104' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Adaptive mutation in E. coli modulated by luxS type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14651' abstract: - lang: eng text: 'For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.' acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651 apa: Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651 chicago: Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651. ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023. ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. mla: Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651. short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023. date_created: 2023-12-11T19:30:37Z date_published: 2023-12-12T00:00:00Z date_updated: 2023-12-22T11:04:45Z day: '12' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:14651 ec_funded: 1 file: - access_level: open_access checksum: 520bdb61e95e66070e02824947d2c5fa content_type: application/pdf creator: larathoo date_created: 2023-12-13T15:37:55Z date_updated: 2023-12-13T15:37:55Z file_id: '14684' file_name: Phd_Thesis_LA.pdf file_size: 34101468 relation: main_file success: 1 - access_level: closed checksum: d8e59afd0817c98fba2564a264508e5c content_type: application/zip creator: larathoo date_created: 2023-12-13T15:42:23Z date_updated: 2023-12-14T08:58:18Z file_id: '14685' file_name: Phd_Thesis_LA.zip file_size: 31052872 relation: source_file - access_level: closed checksum: 9a778c949932286f4519e1f1fca2820d content_type: application/zip creator: larathoo date_created: 2023-12-11T19:24:59Z date_updated: 2023-12-14T08:58:18Z file_id: '14681' file_name: Supplementary_Materials.zip file_size: 10713896 relation: supplementary_material file_date_updated: 2023-12-14T08:58:18Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '96' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14687' abstract: - lang: eng text: The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity. article_number: e202316476 article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Bhargavi full_name: Pant, Bhargavi id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112 last_name: Pant - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 2023. doi:10.1002/anie.202316476 apa: Jethwa, R. B., Mondal, S., Pant, B., & Freunberger, S. A. (2023). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202316476 chicago: Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202316476. ieee: R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” Angewandte Chemie International Edition. Wiley, 2023. ista: Jethwa RB, Mondal S, Pant B, Freunberger SA. 2023. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition., e202316476. mla: Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition, e202316476, Wiley, 2023, doi:10.1002/anie.202316476. short: R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition (2023). date_created: 2023-12-15T16:10:13Z date_published: 2023-12-14T00:00:00Z date_updated: 2024-02-15T14:43:05Z day: '14' department: - _id: StFr - _id: GradSch doi: 10.1002/anie.202316476 keyword: - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1002/anie.202316476' month: '12' oa: 1 oa_version: Published Version publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14697' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp citation: ama: 'Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697' apa: 'Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697' chicago: 'Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.' ieee: 'J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.' ista: 'Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.' mla: 'Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697.' short: 'J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.' date_created: 2023-12-18T19:14:28Z date_published: 2023-12-20T00:00:00Z date_updated: 2023-12-21T14:30:02Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/at:ista:14697 ec_funded: 1 file: - access_level: closed checksum: 457927165d5d556305d3086f6b83e5c7 content_type: application/pdf creator: jstopp date_created: 2023-12-20T09:35:34Z date_updated: 2023-12-20T09:35:34Z embargo: 2024-12-20 embargo_to: open_access file_id: '14699' file_name: Thesis.pdf file_size: 51585778 relation: main_file - access_level: closed checksum: e8d26449ac461f5e8478a62c9507506f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jstopp date_created: 2023-12-20T09:35:35Z date_updated: 2023-12-20T10:41:42Z file_id: '14700' file_name: Thesis.docx file_size: 69625950 relation: source_file file_date_updated: 2023-12-20T10:41:42Z has_accepted_license: '1' language: - iso: eng month: '12' oa_version: Published Version page: '226' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-038-1 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6328' relation: part_of_dissertation status: public - id: '7885' relation: part_of_dissertation status: public - id: '12272' relation: part_of_dissertation status: public - id: '14274' relation: part_of_dissertation status: public - id: '14360' 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: 0000-0002-6620-9179 title: 'Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14703' abstract: - lang: eng text: We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation. acknowledgement: "The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council." article_number: '2312.12213' article_processing_charge: No arxiv: 1 author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida - first_name: Hugo full_name: Lavenant, Hugo last_name: Lavenant citation: ama: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213 apa: Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213 chicago: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213. ieee: S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. . ista: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213. mla: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213. short: S. Ishida, H. Lavenant, ArXiv (n.d.). date_created: 2023-12-21T10:14:37Z date_published: 2023-12-19T00:00:00Z date_updated: 2023-12-27T13:44:33Z day: '19' department: - _id: GradSch - _id: ChWo doi: 10.48550/arXiv.2312.12213 external_id: arxiv: - '2312.12213' keyword: - Optimal transport - Hamilton-Jacobi equation - convex optimization language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.12213 month: '12' oa: 1 oa_version: Preprint project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: arXiv publication_status: submitted status: public title: Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation type: preprint user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14735' abstract: - lang: eng text: "Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs." acknowledgement: 'Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Christos full_name: Stefo, Christos id: a20e8902-32b0-11ee-9fa8-b23fa638b793 last_name: Stefo - first_name: Zhuolun full_name: Xiang, Zhuolun last_name: Xiang - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: 'Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1' apa: 'Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1' chicago: Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1. ieee: C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20. ista: 'Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.' mla: Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1. short: C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-08T09:17:38Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T09:28:14Z day: '01' department: - _id: ElKo - _id: GradSch doi: 10.1007/978-3-031-47754-6_1 intvolume: ' 13950' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2022/1554 month: '12' oa: 1 oa_version: Preprint page: 3-20 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477546' eissn: - 0302-9743 isbn: - '9783031477539' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Executing and proving over dirty ledgers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13950 year: '2023' ... --- _id: '14863' article_number: EGU23-6157 article_processing_charge: No author: - first_name: Andrea full_name: Polesello, Andrea id: 74c777f4-32da-11ee-b498-874db0835561 last_name: Polesello - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Claudia full_name: Pasquero, Claudia last_name: Pasquero - first_name: Agostino N. full_name: Meroni, Agostino N. last_name: Meroni citation: ama: 'Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6157' apa: 'Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157' chicago: Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157. ieee: A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023. ista: Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157. mla: Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6157. short: A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:08:12Z date_published: 2023-04-13T00:00:00Z date_updated: 2024-01-24T11:25:07Z day: '13' ddc: - '550' department: - _id: CaMu - _id: GradSch doi: 10.5194/egusphere-egu23-6157 file: - access_level: open_access checksum: 8cb88c1bc80ccee328478a62064d98f7 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:19:54Z date_updated: 2024-01-24T11:19:54Z file_id: '14883' file_name: 2023_EGU_Polesello.pdf file_size: 296769 relation: main_file success: 1 file_date_updated: 2024-01-24T11:19:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Intensification mechanisms of tropical cyclones 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: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '15039' abstract: - lang: eng text: 'A crucial property for achieving secure, trustworthy and interpretable deep learning systems is their robustness: small changes to a system''s inputs should not result in large changes to its outputs. Mathematically, this means one strives for networks with a small Lipschitz constant. Several recent works have focused on how to construct such Lipschitz networks, typically by imposing constraints on the weight matrices. In this work, we study an orthogonal aspect, namely the role of the activation function. We show that commonly used activation functions, such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily restrict the class of representable functions, even in the simplest one-dimensional setting. We furthermore introduce the new N-activation function that is provably more expressive than currently popular activation functions. We provide code at this https URL.' article_number: '2311.06103' article_processing_charge: No arxiv: 1 author: - first_name: Bernd full_name: Prach, Bernd id: 2D561D42-C427-11E9-89B4-9C1AE6697425 last_name: Prach - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv. doi:10.48550/ARXIV.2311.06103 apa: Prach, B., & Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive with N-activations. arXiv. https://doi.org/10.48550/ARXIV.2311.06103 chicago: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2311.06103. ieee: B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive with N-activations,” arXiv. . ista: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv, 2311.06103. mla: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, 2311.06103, doi:10.48550/ARXIV.2311.06103. short: B. Prach, C. Lampert, ArXiv (n.d.). date_created: 2024-02-28T17:59:32Z date_published: 2023-11-10T00:00:00Z date_updated: 2024-03-04T07:02:39Z day: '10' department: - _id: GradSch - _id: ChLa doi: 10.48550/ARXIV.2311.06103 external_id: arxiv: - '2311.06103' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.06103 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 1-Lipschitz neural networks are more expressive with N-activations type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13053' abstract: - lang: eng text: 'Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .' acknowledged_ssus: - _id: ScienComp acknowledgement: "AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-" article_processing_charge: No arxiv: 1 author: - first_name: Elena-Alexandra full_name: Peste, Elena-Alexandra id: 32D78294-F248-11E8-B48F-1D18A9856A87 last_name: Peste - first_name: Adrian full_name: Vladu, Adrian last_name: Vladu - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .' apa: 'Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .' chicago: 'Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.' ieee: 'E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .' ista: 'Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.' mla: 'Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .' short: E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d. conference: end_date: 2023-05-05 location: 'Kigali, Rwanda ' name: 'ICLR: International Conference on Learning Representations' start_date: 2023-05-01 date_created: 2023-05-23T11:36:18Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-06-01T12:54:45Z department: - _id: GradSch - _id: DaAl - _id: ChLa ec_funded: 1 external_id: arxiv: - '2207.14200' language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/pdf?id=_eTZBs-yedr month: '05' oa: 1 oa_version: Preprint project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: '11th International Conference on Learning Representations ' publication_status: accepted quality_controlled: '1' related_material: record: - id: '13074' relation: dissertation_contains status: public status: public title: 'CrAM: A Compression-Aware Minimizer' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13074' abstract: - lang: eng text: "Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Elena-Alexandra full_name: Peste, Elena-Alexandra id: 32D78294-F248-11E8-B48F-1D18A9856A87 last_name: Peste citation: ama: Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074 apa: Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074 chicago: Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074. ieee: E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023. ista: Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. mla: Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074. short: E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023. date_created: 2023-05-23T17:07:53Z date_published: 2023-05-23T00:00:00Z date_updated: 2023-08-04T10:33:27Z day: '23' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: ChLa doi: 10.15479/at:ista:13074 ec_funded: 1 file: - access_level: open_access checksum: 6b3354968403cb9d48cc5a83611fb571 content_type: application/pdf creator: epeste date_created: 2023-05-24T16:11:16Z date_updated: 2023-05-24T16:11:16Z file_id: '13087' file_name: PhD_Thesis_Alexandra_Peste_final.pdf file_size: 2152072 relation: main_file success: 1 - access_level: closed checksum: 8d0df94bbcf4db72c991f22503b3fd60 content_type: application/zip creator: epeste date_created: 2023-05-24T16:12:59Z date_updated: 2023-05-24T16:12:59Z file_id: '13088' file_name: PhD_Thesis_APeste.zip file_size: 1658293 relation: source_file file_date_updated: 2023-05-24T16:12:59Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _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: '11458' relation: part_of_dissertation status: public - id: '13053' relation: part_of_dissertation status: public - id: '12299' 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 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: Efficiency and generalization of sparse neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13081' abstract: - lang: eng text: During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis. acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Bocanegra, Laura id: 4896F754-F248-11E8-B48F-1D18A9856A87 last_name: Bocanegra citation: ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081 apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081 chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081. ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023. ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081. short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023. date_created: 2023-05-23T19:10:42Z date_published: 2023-05-23T00:00:00Z date_updated: 2023-10-04T11:14:04Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi doi: 10.15479/at:ista:13081 file: - access_level: closed checksum: 74f3f89e59a0189bee53ebfad9c1b9af content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lbocaneg date_created: 2023-05-25T06:32:12Z date_updated: 2023-05-25T06:32:12Z file_id: '13089' file_name: Thesis_final_LauraBocanegra.docx file_size: 25615534 relation: source_file - access_level: closed checksum: c6cdef6323eacfb4b7a8af20f32eae97 content_type: application/pdf creator: lbocaneg date_created: 2023-05-25T06:32:16Z date_updated: 2023-05-25T06:32:16Z embargo: 2024-05-31 embargo_to: open_access file_id: '13090' file_name: TotalFinal_Thesis_LauraBocanegraArx.pdf file_size: 12386046 relation: main_file file_date_updated: 2023-05-25T06:32:16Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '93' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9349' relation: part_of_dissertation status: public - id: '12837' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Epithelial dynamics during mouse neural tube development tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13107' abstract: - lang: eng text: "Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus citation: ama: 'Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107' apa: 'Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107' chicago: 'Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.' ieee: 'L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.' ista: 'Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.' mla: 'Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.' short: 'L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.' date_created: 2023-06-01T09:05:24Z date_published: 2023-05-31T00:00:00Z date_updated: 2024-02-07T08:03:33Z day: '31' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/at:ista:13107 ec_funded: 1 file: - access_level: closed checksum: 4b69a4ac0bbf4163d59c0b58dcb4f2c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lknaus date_created: 2023-06-01T13:48:41Z date_updated: 2023-06-01T13:48:41Z file_id: '13112' file_name: Thesis_Lisa Knaus_approved_final.docx file_size: 12991551 relation: source_file - access_level: open_access checksum: 6903d152aa01181d87a696085af31c83 content_type: application/pdf creator: lknaus date_created: 2023-06-02T09:47:29Z date_updated: 2023-06-07T08:41:49Z file_id: '13114' file_name: Thesis_Lisa Knaus_approved_final_pdfa2b.pdf file_size: 9309015 relation: main_file file_date_updated: 2023-06-07T08:41:49Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: 'The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13120' abstract: - lang: eng text: 'We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.' acknowledgement: "Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. " alternative_title: - LIPIcs article_number: '15' article_processing_charge: No arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Jasmin full_name: Blanchette, Jasmin last_name: Blanchette citation: ama: 'Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15' apa: 'Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15' chicago: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15. ieee: M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268. ista: 'Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.' mla: Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15. short: M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. conference: end_date: 2023-08-04 location: Bialystok, Poland name: 'ITP: International Conference on Interactive Theorem Proving' start_date: 2023-07-31 date_created: 2023-06-05T07:29:05Z date_published: 2023-07-27T00:00:00Z date_updated: 2023-09-25T11:04:29Z day: '27' ddc: - '000' department: - _id: GradSch - _id: VlKo doi: 10.4230/LIPIcs.ITP.2023.15 external_id: arxiv: - '2302.06420' file: - access_level: open_access checksum: 773a0197f05b67feaa6cb1e17ec3642d content_type: application/pdf creator: dernst date_created: 2023-08-07T11:55:43Z date_updated: 2023-08-07T11:55:43Z file_id: '13982' file_name: 2023_LIPIcS_Dvorak.pdf file_size: 715976 relation: main_file success: 1 file_date_updated: 2023-08-07T11:55:43Z has_accepted_license: '1' intvolume: ' 268' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: 14th International Conference on Interactive Theorem Proving publication_identifier: eissn: - 1868-8969 isbn: - '9783959772846' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: link: - relation: software url: https://github.com/madvorak/grammars/tree/publish scopus_import: '1' status: public title: Closure properties of general grammars - formally verified tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 268 year: '2023' ... --- _id: '13128' abstract: - lang: eng text: "Given A⊆GL2(Fq), we prove that there exist disjoint subsets B,C⊆A such that A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where\r\nM(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.\r\n We also study some related questions on moderate expanders over matrix rings, namely, for A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, ForumMath., 31, 951–970).\r\n" article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Ali full_name: Mohammadi, Ali last_name: Mohammadi - first_name: Thang full_name: Pham, Thang last_name: Pham - first_name: Yiting full_name: Wang, Yiting id: 1917d194-076e-11ed-97cd-837255f88785 last_name: Wang orcid: 0000-0002-2856-767X citation: ama: Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 2023;66(4):1280-1295. doi:10.4153/S000843952300036X apa: Mohammadi, A., Pham, T., & Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. Cambridge University Press. https://doi.org/10.4153/S000843952300036X chicago: Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin. Cambridge University Press, 2023. https://doi.org/10.4153/S000843952300036X. ieee: A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” Canadian Mathematical Bulletin, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023. ista: Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295. mla: Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:10.4153/S000843952300036X. short: A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295. date_created: 2023-06-11T22:00:40Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-29T11:00:46Z day: '01' department: - _id: GradSch doi: 10.4153/S000843952300036X external_id: arxiv: - '2106.07328' isi: - '001011963000001' intvolume: ' 66' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2106.07328 month: '12' oa: 1 oa_version: Preprint page: 1280-1295 publication: Canadian Mathematical Bulletin publication_identifier: eissn: - 1496-4287 issn: - 0008-4395 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: An energy decomposition theorem for matrices and related questions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2023' ... --- _id: '13138' abstract: - lang: eng text: "We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain." acknowledgement: "The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. " article_number: '184312' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Pavel full_name: Orlov, Pavel last_name: Orlov - first_name: Anastasiia full_name: Tiutiakina, Anastasiia last_name: Tiutiakina - first_name: Rustem full_name: Sharipov, Rustem last_name: Sharipov - first_name: Elena full_name: Petrova, Elena id: 0ac84990-897b-11ed-a09c-f5abb56a4ede last_name: Petrova - first_name: Vladimir full_name: Gritsev, Vladimir last_name: Gritsev - first_name: Denis V. full_name: Kurlov, Denis V. last_name: Kurlov citation: ama: Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312 apa: Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312 chicago: Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312. ieee: P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023. ista: Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312. mla: Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312. short: P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023). date_created: 2023-06-18T22:00:46Z date_published: 2023-05-01T00:00:00Z date_updated: 2023-08-02T06:16:02Z day: '01' department: - _id: GradSch doi: 10.1103/PhysRevB.107.184312 external_id: arxiv: - '2303.00729' isi: - '001003686900004' intvolume: ' 107' isi: 1 issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2303.00729 month: '05' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 107 year: '2023' ... --- _id: '13166' abstract: - lang: eng text: Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans. acknowledgement: "We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.)." article_number: '9382' article_processing_charge: No article_type: original author: - first_name: Alexandra A. full_name: Vetrova, Alexandra A. last_name: Vetrova - first_name: Daria M. full_name: Kupaeva, Daria M. last_name: Kupaeva - first_name: Alena full_name: Kizenko, Alena id: a521c60b-0815-11ed-9b02-b8bd522477c8 last_name: Kizenko - first_name: Tatiana S. full_name: Lebedeva, Tatiana S. last_name: Lebedeva - first_name: Peter full_name: Walentek, Peter last_name: Walentek - first_name: Nikoloz full_name: Tsikolia, Nikoloz last_name: Tsikolia - first_name: Stanislav V. full_name: Kremnyov, Stanislav V. last_name: Kremnyov citation: ama: Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8 apa: Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8 chicago: Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8. ieee: A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023. ista: Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382. mla: Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8. short: A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023). date_created: 2023-06-25T22:00:46Z date_published: 2023-06-09T00:00:00Z date_updated: 2023-08-02T06:17:18Z day: '09' ddc: - '570' department: - _id: GradSch doi: 10.1038/s41598-023-35979-8 external_id: isi: - '001006690200045' pmid: - '37296138' file: - access_level: open_access checksum: baddf6b2fa9adf88263d4a3b0998f0f2 content_type: application/pdf creator: dernst date_created: 2023-06-26T09:58:53Z date_updated: 2023-06-26T09:58:53Z file_id: '13170' file_name: 2023_ScientificReports_Vetrova.pdf file_size: 4844149 relation: main_file success: 1 file_date_updated: 2023-06-26T09:58:53Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: eissn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2023' ...