[{"ddc":["530"],"abstract":[{"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.","lang":"eng"}],"day":"16","degree_awarded":"PhD","doi":"10.15479/14547","year":"2023","citation":{"mla":"Phan, Duc T. <i>Resonant Microwave Spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>.","short":"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.","apa":"Phan, D. T. (2023). <i>Resonant microwave spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>."},"date_updated":"2023-11-30T10:56:04Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-11-22T09:46:06Z","page":"80","title":"Resonant microwave spectroscopy of Al-InAs","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"date_created":"2023-11-17T13:45:26Z","publication_status":"published","author":[{"last_name":"Phan","first_name":"Duc T","full_name":"Phan, Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"14547","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10851"},{"status":"public","id":"13264","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","file":[{"date_created":"2023-11-17T13:36:44Z","checksum":"db0c37d213bc002125bd59690e9db246","file_size":34828019,"date_updated":"2023-11-22T09:46:06Z","file_name":"Phan_Thesis_pdfa.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"14548","creator":"pduc"},{"file_id":"14549","creator":"pduc","access_level":"closed","relation":"source_file","date_updated":"2023-11-17T13:47:54Z","file_name":"dissertation_src.zip","content_type":"application/zip","date_created":"2023-11-17T13:44:53Z","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","file_size":279319709}],"oa":1,"supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham"}],"publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","date_published":"2023-11-16T00:00:00Z","tmp":{"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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"language":[{"iso":"eng"}],"month":"11","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"has_accepted_license":"1"},{"has_accepted_license":"1","month":"11","oa_version":"Published Version","project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"language":[{"iso":"eng"}],"date_published":"2023-11-21T00:00:00Z","type":"dissertation","tmp":{"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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"supervisor":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_identifier":{"issn":["2663 - 337X"]},"status":"public","related_material":{"record":[{"status":"public","id":"11842","relation":"part_of_dissertation"},{"status":"public","id":"14597","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"creator":"amarvegg","file_id":"14626","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"thesis_Marveggio.pdf","date_updated":"2023-11-29T09:09:31Z","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","file_size":2881100,"date_created":"2023-11-29T09:09:31Z"},{"access_level":"open_access","relation":"source_file","file_id":"14627","creator":"amarvegg","date_created":"2023-11-29T09:10:19Z","file_size":10189696,"checksum":"52f28bdf95ec82cff39f3685f9c48e7d","date_updated":"2023-11-29T09:28:30Z","file_name":"Thesis_Marveggio.zip","content_type":"application/zip"}],"author":[{"full_name":"Marveggio, Alice","last_name":"Marveggio","first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425"}],"_id":"14587","alternative_title":["ISTA Thesis"],"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","publication_status":"published","article_processing_charge":"No","date_created":"2023-11-21T11:41:05Z","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"file_date_updated":"2023-11-29T09:28:30Z","page":"228","ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2023-11-30T13:25:03Z","citation":{"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.","mla":"Marveggio, Alice. <i>Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>.","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.","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>","apa":"Marveggio, A. (2023). <i>Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>","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.","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. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>."},"year":"2023","abstract":[{"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.","lang":"eng"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:14587","day":"21","ddc":["515"],"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)."},{"tmp":{"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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","date_published":"2023-11-30T00:00:00Z","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2023-11-30T15:53:10Z","embargo":"2024-11-30","file_size":11947523,"checksum":"068fd3570506ec42b2faa390de784bc4","embargo_to":"open_access","date_updated":"2023-12-01T11:10:46Z","content_type":"application/pdf","file_name":"PhD_Thesis.pdf","access_level":"closed","relation":"main_file","file_id":"14635","creator":"ssack"},{"file_name":"PhD Thesis (1).zip","content_type":"application/zip","date_updated":"2023-12-01T11:10:46Z","file_size":18422964,"checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","date_created":"2023-11-30T15:54:11Z","creator":"ssack","file_id":"14636","access_level":"closed","relation":"source_file"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11471"},{"relation":"part_of_dissertation","id":"13125","status":"public"},{"relation":"part_of_dissertation","id":"9760","status":"public"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"},{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"oa_version":"Published Version","month":"11","language":[{"iso":"eng"}],"year":"2023","citation":{"chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>","apa":"Sack, S. (2023). <i>Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14622\">https://doi.org/10.15479/at:ista:14622</a>","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. <i>Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14622\">10.15479/at:ista:14622</a>.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023."},"date_updated":"2023-12-13T14:47:25Z","day":"30","doi":"10.15479/at:ista:14622","degree_awarded":"PhD","ddc":["530"],"_id":"14622","author":[{"full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"}],"date_created":"2023-11-28T10:58:13Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","ec_funded":1,"page":"142","file_date_updated":"2023-12-01T11:10:46Z","publisher":"Institute of Science and Technology Austria"},{"keyword":["Computer Graphics and Computer-Aided Design"],"language":[{"iso":"eng"}],"project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"oa_version":"Published Version","article_number":"168","month":"10","has_accepted_license":"1","publication":"ACM Transactions on Graphics","file":[{"date_updated":"2023-11-29T15:16:01Z","file_name":"tog-22-0089-File004.zip","content_type":"application/zip","date_created":"2023-11-29T15:16:01Z","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","file_size":95467870,"file_id":"14630","creator":"yichen","access_level":"open_access","success":1,"relation":"main_file"},{"date_created":"2023-11-29T15:16:01Z","file_size":103731880,"checksum":"7fb024963be81933494f38de191e4710","date_updated":"2023-11-29T15:16:01Z","file_name":"tog-22-0089-File005.zip","content_type":"application/zip","success":1,"relation":"main_file","access_level":"open_access","file_id":"14631","creator":"yichen"},{"checksum":"b7d6829ce396e21cac9fae0ec7130a6b","file_size":57067476,"date_created":"2023-12-04T08:04:14Z","content_type":"application/pdf","file_name":"2023_ACMToG_Makatura.pdf","date_updated":"2023-12-04T08:04:14Z","relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","file_id":"14638"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"issn":["0730-0301","1557-7368"]},"oa":1,"type":"journal_article","date_published":"2023-10-01T00:00:00Z","publisher":"Association for Computing Machinery","article_type":"original","quality_controlled":"1","file_date_updated":"2023-12-04T08:04:14Z","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"date_created":"2023-11-29T15:02:03Z","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","intvolume":"        42","title":"Procedural metamaterials: A unified procedural graph for metamaterial design","_id":"14628","issue":"5","author":[{"last_name":"Makatura","first_name":"Liane","full_name":"Makatura, Liane"},{"full_name":"Wang, Bohan","first_name":"Bohan","last_name":"Wang"},{"first_name":"Yi-Lu","last_name":"Chen","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"full_name":"Deng, Bolei","first_name":"Bolei","last_name":"Deng"},{"last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"}],"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.","volume":42,"ddc":["531","006"],"day":"01","doi":"10.1145/3605389","abstract":[{"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.","lang":"eng"}],"year":"2023","citation":{"apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &#38; Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>","ieee":"L. Makatura <i>et al.</i>, “Procedural metamaterials: A unified procedural graph for metamaterial design,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","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.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>.","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (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."},"date_updated":"2023-12-04T08:09:05Z"},{"doi":"10.15479/at:ista:14641","degree_awarded":"PhD","day":"30","date_updated":"2023-12-07T14:12:25Z","year":"2023","citation":{"mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>.","short":"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.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>."},"ddc":["570"],"publication_status":"published","date_created":"2023-12-04T13:17:37Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"alternative_title":["ISTA Thesis"],"title":"Adaptive mutation in E. coli modulated by luxS","_id":"14641","author":[{"first_name":"Mike","last_name":"Hennessey-Wesen","full_name":"Hennessey-Wesen, Mike","id":"3F338C72-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","page":"104","ec_funded":1,"file_date_updated":"2023-12-06T13:14:15Z","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2023-11-30T00:00:00Z","type":"dissertation","file":[{"access_level":"closed","relation":"source_file","file_id":"14648","creator":"mhenness","date_created":"2023-12-06T13:13:26Z","file_size":46405919,"checksum":"4127c285b34f4bf7fb31ef24f9d14c25","date_updated":"2023-12-06T13:13:26Z","file_name":"mike_thesis_v06-12-2023.odt","content_type":"application/vnd.oasis.opendocument.text"},{"file_id":"14649","creator":"mhenness","relation":"main_file","access_level":"closed","date_updated":"2023-12-06T13:14:15Z","content_type":"application/pdf","file_name":"mike_thesis_v06-12-2023.pdf","embargo":"2024-11-30","date_created":"2023-12-06T13:14:15Z","checksum":"f5203a61eddaf35235bbc51904d73982","file_size":21282155,"embargo_to":"open_access"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"oa_version":"Published Version","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"11","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["microfluidics","miceobiology","mutations","quorum sensing"]},{"ddc":["570"],"date_updated":"2023-12-22T11:04:45Z","citation":{"chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>","apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>."},"year":"2023","degree_awarded":"PhD","doi":"10.15479/at:ista:14651","day":"12","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."}],"page":"96","ec_funded":1,"file_date_updated":"2023-12-14T08:58:18Z","publisher":"Institute of Science and Technology Austria","_id":"14651","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"No","date_created":"2023-12-11T19:30:37Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"alternative_title":["ISTA Thesis"],"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","file":[{"creator":"larathoo","file_id":"14684","relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","file_name":"Phd_Thesis_LA.pdf","date_updated":"2023-12-13T15:37:55Z","checksum":"520bdb61e95e66070e02824947d2c5fa","file_size":34101468,"date_created":"2023-12-13T15:37:55Z"},{"access_level":"closed","relation":"source_file","file_id":"14685","creator":"larathoo","date_created":"2023-12-13T15:42:23Z","file_size":31052872,"checksum":"d8e59afd0817c98fba2564a264508e5c","date_updated":"2023-12-14T08:58:18Z","content_type":"application/zip","file_name":"Phd_Thesis_LA.zip"},{"content_type":"application/zip","file_name":"Supplementary_Materials.zip","date_updated":"2023-12-14T08:58:18Z","file_size":10713896,"checksum":"9a778c949932286f4519e1f1fca2820d","date_created":"2023-12-11T19:24:59Z","creator":"larathoo","file_id":"14681","access_level":"closed","relation":"supplementary_material"}],"related_material":{"record":[{"id":"11411","relation":"part_of_dissertation","status":"public"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2023-12-12T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"12"},{"keyword":["General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"quality_controlled":"1","article_type":"review","publisher":"Wiley","author":[{"full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","last_name":"Jethwa","first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f"},{"first_name":"Soumyadip","last_name":"Mondal","full_name":"Mondal, Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","first_name":"Bhargavi","last_name":"Pant","full_name":"Pant, Bhargavi"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger"}],"scopus_import":"1","_id":"14687","publication":"Angewandte Chemie International Edition","article_number":"e202316476","month":"12","title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"StFr"},{"_id":"GradSch"}],"date_created":"2023-12-15T16:10:13Z","oa_version":"Published Version","publication_status":"epub_ahead","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1002/anie.202316476"}],"type":"journal_article","date_published":"2023-12-14T00:00:00Z","citation":{"ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. 2023. doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>","apa":"Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2023). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>","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,” <i>Angewandte Chemie International Edition</i>. Wiley, 2023.","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.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>.","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition (2023).","mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>, e202316476, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>.","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."},"year":"2023","date_updated":"2024-02-15T14:43:05Z","oa":1,"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."}],"day":"14","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"doi":"10.1002/anie.202316476"},{"title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-12-18T19:14:28Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"article_processing_charge":"No","author":[{"first_name":"Julian A","last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"}],"_id":"14697","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-12-20T10:41:42Z","page":"226","ec_funded":1,"doi":"10.15479/at:ista:14697","degree_awarded":"PhD","day":"20","date_updated":"2023-12-21T14:30:02Z","citation":{"mla":"Stopp, Julian A. <i>Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","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.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","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. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","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."},"year":"2023","ddc":["570"],"month":"12","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]},"date_published":"2023-12-20T00:00:00Z","type":"dissertation","status":"public","related_material":{"record":[{"status":"public","id":"6328","relation":"part_of_dissertation"},{"id":"7885","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12272"},{"relation":"part_of_dissertation","id":"14274","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14360"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"access_level":"closed","relation":"main_file","file_id":"14699","creator":"jstopp","embargo":"2024-12-20","date_created":"2023-12-20T09:35:34Z","embargo_to":"open_access","file_size":51585778,"checksum":"457927165d5d556305d3086f6b83e5c7","date_updated":"2023-12-20T09:35:34Z","file_name":"Thesis.pdf","content_type":"application/pdf"},{"date_created":"2023-12-20T09:35:35Z","file_size":69625950,"checksum":"e8d26449ac461f5e8478a62c9507506f","date_updated":"2023-12-20T10:41:42Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis.docx","access_level":"closed","relation":"source_file","file_id":"14700","creator":"jstopp"}]},{"date_created":"2023-12-21T10:14:37Z","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publication_status":"submitted","oa_version":"Preprint","article_number":"2312.12213","title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","month":"12","_id":"14703","publication":"arXiv","author":[{"full_name":"Ishida, Sadashige","last_name":"Ishida","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"},{"last_name":"Lavenant","first_name":"Hugo","full_name":"Lavenant, Hugo"}],"keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"language":[{"iso":"eng"}],"day":"19","arxiv":1,"doi":"10.48550/arXiv.2312.12213","oa":1,"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."}],"citation":{"chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2312.12213\">https://doi.org/10.48550/arXiv.2312.12213</a>.","ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” <i>arXiv</i>. .","apa":"Ishida, S., &#38; Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2312.12213\">https://doi.org/10.48550/arXiv.2312.12213</a>","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2312.12213\">10.48550/arXiv.2312.12213</a>","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.” <i>ArXiv</i>, 2312.12213, doi:<a href=\"https://doi.org/10.48550/arXiv.2312.12213\">10.48550/arXiv.2312.12213</a>.","short":"S. Ishida, H. Lavenant, ArXiv (n.d.)."},"year":"2023","date_updated":"2023-12-27T13:44:33Z","external_id":{"arxiv":["2312.12213"]},"type":"preprint","date_published":"2023-12-19T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.12213","open_access":"1"}],"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.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public"},{"year":"2023","citation":{"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.” <i>27th International Conference on Financial Cryptography and Data Security</i>, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">10.1007/978-3-031-47754-6_1</a>.","short":"C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20.","chicago":"Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In <i>27th International Conference on Financial Cryptography and Data Security</i>, 13950:3–20. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">https://doi.org/10.1007/978-3-031-47754-6_1</a>.","ieee":"C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in <i>27th International Conference on Financial Cryptography and Data Security</i>, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20.","apa":"Stefo, C., Xiang, Z., &#38; Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In <i>27th International Conference on Financial Cryptography and Data Security</i> (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">https://doi.org/10.1007/978-3-031-47754-6_1</a>","ama":"Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: <i>27th International Conference on Financial Cryptography and Data Security</i>. Vol 13950. Springer Nature; 2023:3-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-47754-6_1\">10.1007/978-3-031-47754-6_1</a>"},"date_updated":"2024-01-08T09:28:14Z","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."}],"day":"01","doi":"10.1007/978-3-031-47754-6_1","volume":13950,"acknowledgement":"Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.","author":[{"id":"a20e8902-32b0-11ee-9fa8-b23fa638b793","first_name":"Christos","last_name":"Stefo","full_name":"Stefo, Christos"},{"full_name":"Xiang, Zhuolun","last_name":"Xiang","first_name":"Zhuolun"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"}],"scopus_import":"1","_id":"14735","intvolume":"     13950","alternative_title":["LNCS"],"title":"Executing and proving over dirty ledgers","article_processing_charge":"No","department":[{"_id":"ElKo"},{"_id":"GradSch"}],"date_created":"2024-01-08T09:17:38Z","publication_status":"published","quality_controlled":"1","page":"3-20","publisher":"Springer Nature","type":"conference","date_published":"2023-12-01T00:00:00Z","oa":1,"publication_identifier":{"issn":["1611-3349"],"eissn":["0302-9743"],"eisbn":["9783031477546"],"isbn":["9783031477539"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://eprint.iacr.org/2022/1554","open_access":"1"}],"publication":"27th International Conference on Financial Cryptography and Data Security","month":"12","project":[{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Secure Network and Hardware for Efficient Blockchains","grant_number":"F8512"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"conference":{"end_date":"2023-05-05","location":"Bol, Brac, Croatia","name":"FC: Financial Cryptography and Data Security","start_date":"2023-05-01"}},{"conference":{"location":"Vienna, Austria & Virtual","end_date":"2023-04-28","start_date":"2023-04-23","name":"EGU General Assembly"},"publisher":"European Geosciences Union","language":[{"iso":"eng"}],"file_date_updated":"2024-01-24T11:19:54Z","article_number":"EGU23-6157","month":"04","title":"Intensification mechanisms of tropical cyclones","date_created":"2024-01-22T12:08:12Z","department":[{"_id":"CaMu"},{"_id":"GradSch"}],"article_processing_charge":"No","publication_status":"published","oa_version":"Published Version","author":[{"full_name":"Polesello, Andrea","last_name":"Polesello","first_name":"Andrea","id":"74c777f4-32da-11ee-b498-874db0835561"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"},{"full_name":"Pasquero, Claudia","first_name":"Claudia","last_name":"Pasquero"},{"first_name":"Agostino N.","last_name":"Meroni","full_name":"Meroni, Agostino N."}],"has_accepted_license":"1","_id":"14863","publication":"EGU General Assembly 2023","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"file":[{"creator":"dernst","file_id":"14883","success":1,"access_level":"open_access","relation":"main_file","file_name":"2023_EGU_Polesello.pdf","content_type":"application/pdf","date_updated":"2024-01-24T11:19:54Z","checksum":"8cb88c1bc80ccee328478a62064d98f7","file_size":296769,"date_created":"2024-01-24T11:19:54Z"}],"oa":1,"day":"13","doi":"10.5194/egusphere-egu23-6157","type":"conference_abstract","date_published":"2023-04-13T00:00:00Z","citation":{"short":"A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023.","mla":"Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” <i>EGU General Assembly 2023</i>, EGU23-6157, European Geosciences Union, 2023, doi:<a href=\"https://doi.org/10.5194/egusphere-egu23-6157\">10.5194/egusphere-egu23-6157</a>.","ista":"Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157.","apa":"Polesello, A., Muller, C. J., Pasquero, C., &#38; Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In <i>EGU General Assembly 2023</i>. Vienna, Austria &#38; Virtual: European Geosciences Union. <a href=\"https://doi.org/10.5194/egusphere-egu23-6157\">https://doi.org/10.5194/egusphere-egu23-6157</a>","ama":"Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: <i>EGU General Assembly 2023</i>. European Geosciences Union; 2023. doi:<a href=\"https://doi.org/10.5194/egusphere-egu23-6157\">10.5194/egusphere-egu23-6157</a>","chicago":"Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In <i>EGU General Assembly 2023</i>. European Geosciences Union, 2023. <a href=\"https://doi.org/10.5194/egusphere-egu23-6157\">https://doi.org/10.5194/egusphere-egu23-6157</a>.","ieee":"A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in <i>EGU General Assembly 2023</i>, Vienna, Austria &#38; Virtual, 2023."},"year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2024-01-24T11:25:07Z"},{"publication":"arXiv","_id":"15039","author":[{"id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","first_name":"Bernd","last_name":"Prach"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","publication_status":"submitted","date_created":"2024-02-28T17:59:32Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"article_processing_charge":"No","title":"1-Lipschitz neural networks are more expressive with N-activations","month":"11","article_number":"2311.06103","language":[{"iso":"eng"}],"date_updated":"2024-03-04T07:02:39Z","citation":{"apa":"Prach, B., &#38; Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive with N-activations. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">https://doi.org/10.48550/ARXIV.2311.06103</a>","ama":"Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">10.48550/ARXIV.2311.06103</a>","chicago":"Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">https://doi.org/10.48550/ARXIV.2311.06103</a>.","ieee":"B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive with N-activations,” <i>arXiv</i>. .","mla":"Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” <i>ArXiv</i>, 2311.06103, doi:<a href=\"https://doi.org/10.48550/ARXIV.2311.06103\">10.48550/ARXIV.2311.06103</a>.","short":"B. Prach, C. Lampert, ArXiv (n.d.).","ista":"Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv, 2311.06103."},"year":"2023","date_published":"2023-11-10T00:00:00Z","external_id":{"arxiv":["2311.06103"]},"type":"preprint","arxiv":1,"doi":"10.48550/ARXIV.2311.06103","day":"10","abstract":[{"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.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.06103","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"language":[{"iso":"eng"}],"quality_controlled":"1","ec_funded":1,"conference":{"location":"Kigali, Rwanda ","end_date":"2023-05-05","name":"ICLR: International Conference on Learning Representations","start_date":"2023-05-01"},"author":[{"full_name":"Peste, Elena-Alexandra","first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vladu, Adrian","last_name":"Vladu","first_name":"Adrian"},{"id":"47beb3a5-07b5-11eb-9b87-b108ec578218","last_name":"Kurtic","first_name":"Eldar","full_name":"Kurtic, Eldar"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"_id":"13053","publication":"11th International Conference on Learning Representations ","title":"CrAM: A Compression-Aware Minimizer","month":"05","article_processing_charge":"No","date_created":"2023-05-23T11:36:18Z","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Preprint","publication_status":"accepted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"13074","relation":"dissertation_contains"}]},"status":"public","main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"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)-","external_id":{"arxiv":["2207.14200"]},"type":"conference","date_published":"2023-05-01T00:00:00Z","year":"2023","citation":{"short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” <i>11th International Conference on Learning Representations </i>.","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.","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., &#38; Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In <i>11th International Conference on Learning Representations </i>. Kigali, Rwanda .","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: <i>11th International Conference on Learning Representations </i>.","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in <i>11th International Conference on Learning Representations </i>, Kigali, Rwanda .","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In <i>11th International Conference on Learning Representations </i>, n.d."},"date_updated":"2023-06-01T12:54:45Z","oa":1,"abstract":[{"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 .","lang":"eng"}],"arxiv":1},{"file_date_updated":"2023-05-24T16:12:59Z","page":"147","ec_funded":1,"publisher":"Institute of Science and Technology Austria","author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste","first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra"}],"_id":"13074","title":"Efficiency and generalization of sparse neural networks","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"article_processing_charge":"No","date_created":"2023-05-23T17:07:53Z","ddc":["000"],"date_updated":"2023-08-04T10:33:27Z","citation":{"ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>.","apa":"Peste, E.-A. (2023). <i>Efficiency and generalization of sparse neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","mla":"Peste, Elena-Alexandra. <i>Efficiency and Generalization of Sparse Neural Networks</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>."},"year":"2023","abstract":[{"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.","lang":"eng"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:13074","day":"23","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"05","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"relation":"part_of_dissertation","id":"11458","status":"public"},{"id":"13053","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12299","status":"public"}]},"status":"public","file":[{"creator":"epeste","file_id":"13087","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","date_updated":"2023-05-24T16:11:16Z","file_size":2152072,"checksum":"6b3354968403cb9d48cc5a83611fb571","date_created":"2023-05-24T16:11:16Z"},{"relation":"source_file","access_level":"closed","creator":"epeste","file_id":"13088","file_size":1658293,"checksum":"8d0df94bbcf4db72c991f22503b3fd60","date_created":"2023-05-24T16:12:59Z","content_type":"application/zip","file_name":"PhD_Thesis_APeste.zip","date_updated":"2023-05-24T16:12:59Z"}],"date_published":"2023-05-23T00:00:00Z","type":"dissertation","supervisor":[{"last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]}},{"ddc":["570"],"year":"2023","citation":{"ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","mla":"Bocanegra, Laura. <i>Epithelial Dynamics during Mouse Neural Tube Development</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>.","short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13081\">10.15479/at:ista:13081</a>","apa":"Bocanegra, L. (2023). <i>Epithelial dynamics during mouse neural tube development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13081\">https://doi.org/10.15479/at:ista:13081</a>"},"date_updated":"2023-10-04T11:14:04Z","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."}],"day":"23","doi":"10.15479/at:ista:13081","degree_awarded":"PhD","file_date_updated":"2023-05-25T06:32:16Z","page":"93","publisher":"Institute of Science and Technology Austria","author":[{"id":"4896F754-F248-11E8-B48F-1D18A9856A87","last_name":"Bocanegra","first_name":"Laura","full_name":"Bocanegra, Laura"}],"_id":"13081","alternative_title":["ISTA Thesis"],"title":"Epithelial dynamics during mouse neural tube development","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"article_processing_charge":"No","date_created":"2023-05-23T19:10:42Z","publication_status":"published","status":"public","related_material":{"record":[{"id":"9349","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"12837","relation":"part_of_dissertation"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"creator":"lbocaneg","file_id":"13089","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_final_LauraBocanegra.docx","date_updated":"2023-05-25T06:32:12Z","file_size":25615534,"checksum":"74f3f89e59a0189bee53ebfad9c1b9af","date_created":"2023-05-25T06:32:12Z"},{"file_id":"13090","creator":"lbocaneg","access_level":"closed","relation":"main_file","date_updated":"2023-05-25T06:32:16Z","file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","content_type":"application/pdf","date_created":"2023-05-25T06:32:16Z","embargo":"2024-05-31","embargo_to":"open_access","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","file_size":12386046}],"type":"dissertation","date_published":"2023-05-23T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"supervisor":[{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"05","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version"},{"date_updated":"2024-02-07T08:03:33Z","citation":{"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. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","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.","apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","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. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","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."},"year":"2023","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."}],"degree_awarded":"PhD","doi":"10.15479/at:ista:13107","day":"31","ddc":["570"],"author":[{"full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"}],"_id":"13107","alternative_title":["ISTA Thesis"],"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","publication_status":"published","date_created":"2023-06-01T09:05:24Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"file_date_updated":"2023-06-07T08:41:49Z","page":"147","ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_published":"2023-05-31T00:00:00Z","type":"dissertation","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"}],"oa":1,"publication_identifier":{"issn":["2663 - 337X"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12802"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"relation":"source_file","access_level":"closed","file_id":"13112","creator":"lknaus","date_created":"2023-06-01T13:48:41Z","file_size":12991551,"checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","date_updated":"2023-06-01T13:48:41Z","file_name":"Thesis_Lisa Knaus_approved_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_created":"2023-06-02T09:47:29Z","checksum":"6903d152aa01181d87a696085af31c83","file_size":9309015,"date_updated":"2023-06-07T08:41:49Z","content_type":"application/pdf","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","relation":"main_file","access_level":"open_access","file_id":"13114","creator":"lknaus"}],"has_accepted_license":"1","month":"05","oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"project":[{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}]},{"file":[{"creator":"dernst","file_id":"13982","success":1,"relation":"main_file","access_level":"open_access","file_name":"2023_LIPIcS_Dvorak.pdf","content_type":"application/pdf","date_updated":"2023-08-07T11:55:43Z","file_size":715976,"checksum":"773a0197f05b67feaa6cb1e17ec3642d","date_created":"2023-08-07T11:55:43Z"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://github.com/madvorak/grammars/tree/publish","relation":"software"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-07-27T00:00:00Z","type":"conference","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772846"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Bialystok, Poland","end_date":"2023-08-04","name":"ITP: International Conference on Interactive Theorem Proving","start_date":"2023-07-31"},"publication":"14th International Conference on Interactive Theorem Proving","has_accepted_license":"1","oa_version":"Published Version","month":"07","article_number":"15","volume":268,"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. ","ddc":["000"],"date_updated":"2023-09-25T11:04:29Z","year":"2023","citation":{"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.” <i>14th International Conference on Interactive Theorem Proving</i>, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">10.4230/LIPIcs.ITP.2023.15</a>.","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in <i>14th International Conference on Interactive Theorem Proving</i>, Bialystok, Poland, 2023, vol. 268.","chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In <i>14th International Conference on Interactive Theorem Proving</i>, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">https://doi.org/10.4230/LIPIcs.ITP.2023.15</a>.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: <i>14th International Conference on Interactive Theorem Proving</i>. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">10.4230/LIPIcs.ITP.2023.15</a>","apa":"Dvorak, M., &#38; Blanchette, J. (2023). Closure properties of general grammars - formally verified. In <i>14th International Conference on Interactive Theorem Proving</i> (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">https://doi.org/10.4230/LIPIcs.ITP.2023.15</a>"},"external_id":{"arxiv":["2302.06420"]},"arxiv":1,"doi":"10.4230/LIPIcs.ITP.2023.15","day":"27","abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","file_date_updated":"2023-08-07T11:55:43Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"13120","scopus_import":"1","author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","last_name":"Dvorak","first_name":"Martin"},{"full_name":"Blanchette, Jasmin","last_name":"Blanchette","first_name":"Jasmin"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"date_created":"2023-06-05T07:29:05Z","title":"Closure properties of general grammars - formally verified","alternative_title":["LIPIcs"],"intvolume":"       268"},{"date_updated":"2024-01-29T11:00:46Z","citation":{"apa":"Mohammadi, A., Pham, T., &#38; Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. 2023;66(4):1280-1295. doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023.","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>.","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>.","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295."},"year":"2023","isi":1,"external_id":{"arxiv":["2106.07328"],"isi":["001011963000001"]},"doi":"10.4153/S000843952300036X","arxiv":1,"day":"01","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"}],"volume":66,"_id":"13128","scopus_import":"1","author":[{"first_name":"Ali","last_name":"Mohammadi","full_name":"Mohammadi, Ali"},{"full_name":"Pham, Thang","first_name":"Thang","last_name":"Pham"},{"id":"1917d194-076e-11ed-97cd-837255f88785","last_name":"Wang","first_name":"Yiting","full_name":"Wang, Yiting","orcid":"0000-0002-2856-767X"}],"issue":"4","publication_status":"published","date_created":"2023-06-11T22:00:40Z","department":[{"_id":"GradSch"}],"article_processing_charge":"No","title":"An energy decomposition theorem for matrices and related questions","intvolume":"        66","page":"1280-1295","quality_controlled":"1","publisher":"Cambridge University Press","article_type":"original","date_published":"2023-12-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"Canadian Mathematical Bulletin","oa_version":"Preprint","month":"12","language":[{"iso":"eng"}]},{"date_published":"2023-05-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.00729","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication":"Physical Review B","oa_version":"Preprint","month":"05","article_number":"184312","language":[{"iso":"eng"}],"date_updated":"2023-08-02T06:16:02Z","year":"2023","citation":{"mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” <i>Physical Review B</i>, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">10.1103/PhysRevB.107.184312</a>.","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (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.","apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., &#38; Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">https://doi.org/10.1103/PhysRevB.107.184312</a>","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. <i>Physical Review B</i>. 2023;107(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">10.1103/PhysRevB.107.184312</a>","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.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">https://doi.org/10.1103/PhysRevB.107.184312</a>.","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,” <i>Physical Review B</i>, vol. 107, no. 18. American Physical Society, 2023."},"isi":1,"external_id":{"arxiv":["2303.00729"],"isi":["001003686900004"]},"arxiv":1,"doi":"10.1103/PhysRevB.107.184312","day":"01","abstract":[{"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.","lang":"eng"}],"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. ","volume":107,"_id":"13138","scopus_import":"1","author":[{"last_name":"Orlov","first_name":"Pavel","full_name":"Orlov, Pavel"},{"full_name":"Tiutiakina, Anastasiia","first_name":"Anastasiia","last_name":"Tiutiakina"},{"first_name":"Rustem","last_name":"Sharipov","full_name":"Sharipov, Rustem"},{"full_name":"Petrova, Elena","first_name":"Elena","last_name":"Petrova","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"full_name":"Gritsev, Vladimir","first_name":"Vladimir","last_name":"Gritsev"},{"full_name":"Kurlov, Denis V.","last_name":"Kurlov","first_name":"Denis V."}],"issue":"18","publication_status":"published","date_created":"2023-06-18T22:00:46Z","department":[{"_id":"GradSch"}],"article_processing_charge":"No","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","intvolume":"       107","quality_controlled":"1","publisher":"American Physical Society","article_type":"original"},{"language":[{"iso":"eng"}],"article_number":"9382","month":"06","oa_version":"Published Version","has_accepted_license":"1","publication":"Scientific Reports","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"13170","creator":"dernst","date_created":"2023-06-26T09:58:53Z","checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","file_size":4844149,"date_updated":"2023-06-26T09:58:53Z","file_name":"2023_ScientificReports_Vetrova.pdf","content_type":"application/pdf"}],"oa":1,"publication_identifier":{"eissn":["2045-2322"]},"type":"journal_article","date_published":"2023-06-09T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","publisher":"Springer Nature","file_date_updated":"2023-06-26T09:58:53Z","quality_controlled":"1","intvolume":"        13","title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","article_processing_charge":"No","department":[{"_id":"GradSch"}],"date_created":"2023-06-25T22:00:46Z","publication_status":"published","author":[{"full_name":"Vetrova, Alexandra A.","last_name":"Vetrova","first_name":"Alexandra A."},{"last_name":"Kupaeva","first_name":"Daria M.","full_name":"Kupaeva, Daria M."},{"id":"a521c60b-0815-11ed-9b02-b8bd522477c8","last_name":"Kizenko","first_name":"Alena","full_name":"Kizenko, Alena"},{"full_name":"Lebedeva, Tatiana S.","last_name":"Lebedeva","first_name":"Tatiana S."},{"full_name":"Walentek, Peter","first_name":"Peter","last_name":"Walentek"},{"full_name":"Tsikolia, Nikoloz","last_name":"Tsikolia","first_name":"Nikoloz"},{"full_name":"Kremnyov, Stanislav V.","last_name":"Kremnyov","first_name":"Stanislav V."}],"scopus_import":"1","_id":"13166","pmid":1,"ddc":["570"],"volume":13,"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.).","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."}],"day":"09","doi":"10.1038/s41598-023-35979-8","external_id":{"isi":["001006690200045"],"pmid":["37296138"]},"isi":1,"year":"2023","citation":{"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.” <i>Scientific Reports</i>, vol. 13, 9382, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35979-8\">10.1038/s41598-023-35979-8</a>.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","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.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35979-8\">https://doi.org/10.1038/s41598-023-35979-8</a>.","ieee":"A. A. Vetrova <i>et al.</i>, “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” <i>Scientific Reports</i>, vol. 13. Springer Nature, 2023.","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. <i>Scientific Reports</i>. 2023;13. doi:<a href=\"https://doi.org/10.1038/s41598-023-35979-8\">10.1038/s41598-023-35979-8</a>","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., &#38; Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35979-8\">https://doi.org/10.1038/s41598-023-35979-8</a>"},"date_updated":"2023-08-02T06:17:18Z"}]