[{"ec_funded":1,"file_date_updated":"2020-07-14T12:48:01Z","year":"2020","department":[{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","last_name":"Forkert","full_name":"Forkert, Dominik L"}],"date_created":"2020-04-02T06:40:23Z","date_updated":"2023-09-07T13:03:12Z","publication_identifier":{"issn":["2663-337X"]},"month":"03","oa":1,"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:7629","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7629","ddc":["510"],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","status":"public","file":[{"relation":"main_file","file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T10:47:59Z","access_level":"open_access","file_name":"Thesis_Forkert_PDFA.pdf","content_type":"application/pdf","file_size":3297129,"creator":"dernst"},{"relation":"source_file","file_id":"7658","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","date_created":"2020-04-14T10:47:59Z","date_updated":"2020-07-14T12:48:01Z","access_level":"closed","file_name":"Thesis_Forkert_source.zip","content_type":"application/x-zip-compressed","file_size":1063908,"creator":"dernst"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"31","citation":{"chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.","mla":"Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629"},"page":"154","date_published":"2020-03-31T00:00:00Z"},{"publication_identifier":{"eissn":["2663-337X"]},"month":"09","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8574","oa":1,"file_date_updated":"2020-09-28T07:25:37Z","date_created":"2020-09-28T07:33:38Z","date_updated":"2023-09-07T13:11:39Z","author":[{"first_name":"Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2020","has_accepted_license":"1","article_processing_charge":"No","day":"20","date_published":"2020-09-20T00:00:00Z","page":"158","citation":{"apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574."},"abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"20e71f015fbbd78fea708893ad634ed0","success":1,"date_created":"2020-09-28T07:25:35Z","date_updated":"2020-09-28T07:25:35Z","relation":"main_file","file_id":"8575","file_size":6354833,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"thesis_EnikoSzep_final.pdf"},{"file_name":"thesisFiles_EnikoSzep.zip","access_level":"closed","creator":"dernst","file_size":23020401,"content_type":"application/x-zip-compressed","file_id":"8576","relation":"source_file","date_created":"2020-09-28T07:25:37Z","date_updated":"2020-09-28T07:25:37Z","checksum":"a8de2c14a1bb4e53c857787efbb289e1"}],"oa_version":"Published Version","status":"public","title":"Local adaptation in metapopulations","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8574"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"doi":"10.15479/AT:ISTA:7514","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"publication_identifier":{"issn":["2663-337X"]},"month":"02","year":"2020","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"7524","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon"}],"date_created":"2020-02-24T09:17:27Z","date_updated":"2023-09-07T13:12:42Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:59Z","citation":{"mla":"Mayer, Simon. The Free Energy of a Dilute Two-Dimensional Bose Gas. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7514.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7514.","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","apa":"Mayer, S. (2020). The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7514","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020."},"page":"148","date_published":"2020-02-24T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"24","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7514","status":"public","title":"The free energy of a dilute two-dimensional Bose gas","ddc":["510"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7515","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-24T09:15:06Z","access_level":"open_access","file_name":"thesis.pdf","content_type":"application/pdf","file_size":1563429,"creator":"dernst"},{"date_created":"2020-02-24T09:15:16Z","date_updated":"2020-07-14T12:47:59Z","checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_id":"7516","relation":"source_file","creator":"dernst","content_type":"application/x-zip-compressed","file_size":2028038,"file_name":"thesis_source.zip","access_level":"closed"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks."}]},{"citation":{"ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","apa":"Steiner, J. (2020). Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8353","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","mla":"Steiner, Julia. Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8353.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8353."},"page":"191","date_published":"2020-09-09T00:00:00Z","day":"09","article_processing_charge":"No","has_accepted_license":"1","_id":"8353","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["572"],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","status":"public","file":[{"creator":"jsteiner","file_size":117547589,"content_type":"application/pdf","file_name":"Thesis_Julia_Steiner_pdfA.pdf","access_level":"open_access","date_updated":"2021-09-16T12:40:56Z","date_created":"2020-09-09T14:22:35Z","checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_id":"8354","relation":"main_file"},{"file_name":"Thesis_Julia_Steiner.docx","access_level":"closed","creator":"jsteiner","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":223328668,"file_id":"8355","relation":"source_file","date_created":"2020-09-09T14:23:25Z","date_updated":"2020-09-15T08:48:37Z","checksum":"ba112f957b7145462d0ab79044873ee9"}],"oa_version":"None","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.","lang":"eng"}],"oa":1,"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"doi":"10.15479/AT:ISTA:8353","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"supervisor":[{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","year":"2020","publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Steiner, Julia","last_name":"Steiner","first_name":"Julia","orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8284","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T13:14:09Z","date_created":"2020-09-09T14:27:01Z","file_date_updated":"2021-09-16T12:40:56Z"},{"file_date_updated":"2021-10-01T13:33:02Z","year":"2020","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7643"}]},"date_created":"2020-09-30T14:50:51Z","date_updated":"2023-09-07T13:13:05Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:8589","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"_id":"8589","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["580"],"title":"Novel insights into PIN polarity regulation during Arabidopsis development","oa_version":"Published Version","file":[{"creator":"dernst","file_size":49198118,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2020_Han_Thesis.docx","checksum":"c4bda1947d4c09c428ac9ce667b02327","date_updated":"2020-09-30T14:50:20Z","date_created":"2020-09-30T14:50:20Z","file_id":"8590","relation":"source_file"},{"access_level":"open_access","file_name":"2020_Han_Thesis.pdf","creator":"dernst","file_size":15513963,"content_type":"application/pdf","file_id":"8591","relation":"main_file","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","date_created":"2020-09-30T14:49:59Z","date_updated":"2021-10-01T13:33:02Z"}],"day":"30","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","apa":"Han, H. (2020). Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8589","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","mla":"Han, Huibin. Novel Insights into PIN Polarity Regulation during Arabidopsis Development. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8589.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8589."},"page":"164","date_published":"2020-09-30T00:00:00Z"},{"date_published":"2020-07-24T00:00:00Z","page":"310","citation":{"ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:10.15479/AT:ISTA:8155","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.","mla":"Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020."},"has_accepted_license":"1","article_processing_charge":"No","day":"24","file":[{"file_size":16638998,"content_type":"application/pdf","creator":"rgrah","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","access_level":"open_access","date_updated":"2020-07-27T12:00:07Z","date_created":"2020-07-27T12:00:07Z","success":1,"relation":"main_file","file_id":"8176"},{"content_type":"application/zip","file_size":347459978,"creator":"rgrah","file_name":"Thesis_new.zip","access_level":"closed","date_updated":"2020-07-30T13:04:55Z","date_created":"2020-07-27T12:02:23Z","relation":"main_file","file_id":"8177"}],"oa_version":"Published Version","title":"Gene regulation across scales – how biophysical constraints shape evolution","status":"public","ddc":["530","570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8155","abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"doi":"10.15479/AT:ISTA:8155","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"07","date_updated":"2023-09-07T13:13:27Z","date_created":"2020-07-23T09:51:28Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7675"},{"id":"7569","relation":"part_of_dissertation","status":"public"},{"id":"7652","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","first_name":"Rok"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","file_date_updated":"2020-07-30T13:04:55Z"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"_id":"7460","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The hole system of triangulated shapes","status":"public","ddc":["514"],"file":[{"content_type":"application/pdf","file_size":76195184,"creator":"koelsboe","file_name":"thesis_ist-final_noack.pdf","access_level":"open_access","date_created":"2020-02-06T14:43:54Z","date_updated":"2020-07-14T12:47:58Z","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","relation":"main_file","file_id":"7461"},{"file_size":122103715,"content_type":"application/x-zip-compressed","creator":"koelsboe","access_level":"closed","file_name":"latex-files.zip","description":"latex source files, figures","checksum":"7a52383c812b0be64d3826546509e5a4","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-06T14:52:45Z","relation":"source_file","file_id":"7462"}],"oa_version":"Published Version","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"has_accepted_license":"1","article_processing_charge":"No","day":"10","citation":{"ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460."},"page":"155","date_published":"2020-02-10T00:00:00Z","file_date_updated":"2020-07-14T12:47:58Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"publication_status":"published","related_material":{"record":[{"id":"6608","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Ölsböck, Katharina","first_name":"Katharina","last_name":"Ölsböck","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297"}],"date_updated":"2023-09-07T13:15:30Z","date_created":"2020-02-06T14:56:53Z","publication_identifier":{"issn":["2663-337X"]},"month":"02","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/AT:ISTA:7460","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD"},{"day":"25","has_accepted_license":"1","article_processing_charge":"No","date_published":"2020-05-25T00:00:00Z","citation":{"mla":"Kamath Hosdurg, Chethan. On the Average-Case Hardness of Total Search Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7896.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7896.","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:10.15479/AT:ISTA:7896","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","apa":"Kamath Hosdurg, C. (2020). On the average-case hardness of total search problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7896","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020."},"page":"126","abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"checksum":"b39e2e1c376f5819b823fb7077491c64","date_updated":"2020-07-14T12:48:04Z","date_created":"2020-05-26T14:08:13Z","file_id":"7897","relation":"main_file","creator":"dernst","file_size":1622742,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_Thesis_Kamath.pdf"},{"file_id":"7898","relation":"source_file","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","date_created":"2020-05-26T14:08:23Z","date_updated":"2020-07-14T12:48:04Z","access_level":"closed","file_name":"Thesis_Kamath.zip","creator":"dernst","content_type":"application/x-zip-compressed","file_size":15301529}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7896","status":"public","ddc":["000"],"title":"On the average-case hardness of total search problems","month":"05","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:7896","degree_awarded":"PhD","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"file_date_updated":"2020-07-14T12:48:04Z","ec_funded":1,"author":[{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"}],"related_material":{"record":[{"id":"6677","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T13:15:55Z","date_created":"2020-05-26T14:08:55Z","year":"2020","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria"},{"page":"160","citation":{"ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020."},"date_published":"2020-06-09T00:00:00Z","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"has_accepted_license":"1","article_processing_charge":"No","day":"09","status":"public","title":"Reconfiguration problems","ddc":["516","514"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7944","oa_version":"Published Version","file":[{"file_name":"THESIS_Zuzka_Masarova.pdf","access_level":"open_access","creator":"zmasarov","file_size":13661779,"content_type":"application/pdf","file_id":"7945","relation":"main_file","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-08T00:34:00Z","checksum":"df688bc5a82b50baee0b99d25fc7b7f0"},{"access_level":"closed","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","creator":"zmasarov","content_type":"application/zip","file_size":32184006,"file_id":"7946","relation":"source_file","checksum":"45341a35b8f5529c74010b7af43ac188","date_updated":"2020-07-14T12:48:05Z","date_created":"2020-06-08T00:35:30Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"oa":1,"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7944","publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"month":"06","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","date_created":"2020-06-08T00:49:46Z","date_updated":"2023-09-07T13:17:37Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7950"},{"id":"5986","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","file_date_updated":"2020-07-14T12:48:05Z"},{"author":[{"full_name":"Bezeljak, Urban","first_name":"Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7580"}]},"date_created":"2020-09-08T08:53:53Z","date_updated":"2023-09-07T13:17:06Z","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","year":"2020","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-16T12:49:12Z","doi":"10.15479/AT:ISTA:8341","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"degree_awarded":"PhD","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"month":"09","publication_identifier":{"issn":["2663-337X"]},"file":[{"file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","access_level":"closed","file_size":65246782,"content_type":"application/x-zip-compressed","creator":"dernst","relation":"source_file","file_id":"8342","date_updated":"2021-09-16T12:49:12Z","date_created":"2020-09-08T09:00:29Z","checksum":"70871b335a595252a66c6bbf0824fb02"},{"file_name":"2020_Urban_Bezeljak_Thesis.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":31259058,"file_id":"8343","relation":"main_file","date_created":"2020-09-08T09:00:27Z","date_updated":"2021-09-16T12:49:12Z","checksum":"59a62275088b00b7241e6ff4136434c7"}],"oa_version":"Published Version","_id":"8341","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"In vitro reconstitution of a Rab activation switch","status":"public","ddc":["570"],"abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2020-09-08T00:00:00Z","citation":{"short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria."},"page":"215","day":"08","article_processing_charge":"No","has_accepted_license":"1"},{"date_published":"2020-06-26T00:00:00Z","page":"xviii+120","citation":{"ama":"Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032","ista":"Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria.","ieee":"K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020.","apa":"Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032","mla":"Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032.","short":"K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020.","chicago":"Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032."},"day":"26","article_processing_charge":"No","has_accepted_license":"1","file":[{"access_level":"open_access","file_name":"Kristof_Huszar-Thesis.pdf","creator":"khuszar","file_size":2637562,"content_type":"application/pdf","file_id":"8034","relation":"main_file","checksum":"bd8be6e4f1addc863dfcc0fad29ee9c3","date_created":"2020-06-26T10:03:58Z","date_updated":"2020-07-14T12:48:08Z"},{"date_updated":"2020-07-14T12:48:08Z","date_created":"2020-06-26T10:10:06Z","checksum":"d5f8456202b32f4a77552ef47a2837d1","file_id":"8035","relation":"source_file","creator":"khuszar","file_size":7163491,"content_type":"application/x-zip-compressed","file_name":"Kristof_Huszar-Thesis-source.zip","access_level":"closed"}],"oa_version":"Published Version","status":"public","ddc":["514"],"title":"Combinatorial width parameters for 3-dimensional manifolds","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8032","abstract":[{"lang":"eng","text":"Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","last_name":"Spreer","full_name":"Spreer, Jonathan"}],"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"CampIT"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8032","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-006-0"]},"date_updated":"2023-09-07T13:18:27Z","date_created":"2020-06-26T10:00:36Z","author":[{"full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","last_name":"Huszár","first_name":"Kristóf"}],"related_material":{"record":[{"id":"6556","status":"public","relation":"dissertation_contains"},{"id":"7093","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"year":"2020","file_date_updated":"2020-07-14T12:48:08Z"},{"publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:8358","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}],"degree_awarded":"PhD","file_date_updated":"2020-09-11T07:48:10Z","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","year":"2020","department":[{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7572"},{"id":"7197","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R"}],"date_created":"2020-09-10T09:26:49Z","date_updated":"2023-09-07T13:18:51Z","has_accepted_license":"1","article_processing_charge":"No","day":"10","citation":{"mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358"},"page":"135","date_published":"2020-09-10T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8358","ddc":["572"],"title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","status":"public","file":[{"relation":"main_file","file_id":"8364","checksum":"882f93fe9c351962120e2669b84bf088","success":1,"date_updated":"2020-09-10T12:11:29Z","date_created":"2020-09-10T12:11:29Z","access_level":"open_access","file_name":"phd_thesis_pcaldas.pdf","content_type":"application/pdf","file_size":141602462,"creator":"pcaldas"},{"access_level":"closed","file_name":"phd_thesis_latex_pcaldas.zip","creator":"pcaldas","content_type":"application/x-zip-compressed","file_size":450437458,"file_id":"8365","relation":"source_file","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","date_created":"2020-09-10T12:18:17Z","date_updated":"2020-09-11T07:48:10Z"}],"oa_version":"Published Version"},{"abstract":[{"text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_id":"8333","relation":"main_file","date_updated":"2020-09-04T12:17:47Z","date_created":"2020-09-04T12:17:47Z","checksum":"26fe261550f691280bda4c454bf015c7","file_name":"kragl-thesis.pdf","access_level":"open_access","creator":"bkragl","content_type":"application/pdf","file_size":1348815},{"creator":"bkragl","file_size":372312,"content_type":"application/zip","file_name":"kragl-thesis.zip","access_level":"closed","date_updated":"2020-09-04T13:00:17Z","date_created":"2020-09-04T13:00:17Z","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","relation":"source_file"}],"_id":"8332","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","status":"public","day":"03","article_processing_charge":"No","has_accepted_license":"1","date_published":"2020-09-03T00:00:00Z","citation":{"short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria."},"page":"120","file_date_updated":"2020-09-04T13:00:17Z","author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"133"},{"relation":"part_of_dissertation","status":"public","id":"8012"},{"status":"public","relation":"part_of_dissertation","id":"8195"},{"id":"160","relation":"part_of_dissertation","status":"public"}]},"date_created":"2020-09-04T12:24:12Z","date_updated":"2023-09-13T08:45:08Z","year":"2020","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","month":"09","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8332","supervisor":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1},{"supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:8958","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"oa":1,"month":"12","publication_identifier":{"issn":["2663-337X"]},"date_created":"2020-12-21T09:44:30Z","date_updated":"2023-09-20T11:30:58Z","author":[{"full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Xiang"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5886"},{"status":"public","relation":"part_of_dissertation","id":"8587"},{"id":"1120","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiLe"}],"year":"2020","file_date_updated":"2020-12-30T07:18:03Z","ec_funded":1,"date_published":"2020-12-21T00:00:00Z","page":"125","citation":{"apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958."},"day":"21","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"THESIS_Xiang_Li.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3622305,"creator":"xli","relation":"main_file","file_id":"8967","date_updated":"2020-12-22T10:55:56Z","date_created":"2020-12-22T10:55:56Z","checksum":"3994c54a1241451d561db1d4f43bad30","success":1},{"date_created":"2020-12-22T10:56:03Z","date_updated":"2020-12-30T07:18:03Z","checksum":"0954ecfc5554c05615c14de803341f00","relation":"source_file","file_id":"8968","content_type":"application/x-zip-compressed","file_size":4018859,"creator":"xli","file_name":"THESIS_Xiang_Li.zip","access_level":"closed"}],"oa_version":"Published Version","ddc":["539"],"title":"Rotation of coupled cold molecules in the presence of a many-body environment","status":"public","_id":"8958","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"page":"148","citation":{"chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020.","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386"},"date_published":"2020-09-14T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"14","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","ddc":["003"],"status":"public","_id":"8386","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"8388","relation":"source_file","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","date_created":"2020-09-14T01:02:59Z","date_updated":"2020-09-14T12:18:43Z","access_level":"closed","file_name":"Thesis_Ran.zip","creator":"rzhang","content_type":"application/x-zip-compressed","file_size":1245800191},{"date_updated":"2020-09-15T12:51:53Z","date_created":"2020-09-15T12:51:53Z","checksum":"817e20c33be9247f906925517c56a40d","success":1,"relation":"main_file","file_id":"8396","file_size":161385316,"content_type":"application/pdf","creator":"rzhang","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","access_level":"open_access"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.","lang":"eng"}],"project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.15479/AT:ISTA:8386","publication_identifier":{"issn":["2663-337X"]},"month":"09","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeBi"}],"publication_status":"published","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","year":"2020","date_created":"2020-09-14T01:04:53Z","date_updated":"2023-09-22T09:49:31Z","related_material":{"record":[{"id":"486","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1002"}]},"author":[{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3808-281X","first_name":"Ran","last_name":"Zhang","full_name":"Zhang, Ran"}],"ec_funded":1,"file_date_updated":"2020-09-15T12:51:53Z"},{"department":[{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","date_updated":"2023-09-26T15:50:22Z","date_created":"2020-06-22T09:22:23Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1328"},{"id":"7541","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"77"},{"id":"23","relation":"part_of_dissertation","status":"public"},{"id":"840","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Kukucka, Josip","last_name":"Kukucka","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:48:07Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7996","publication_identifier":{"issn":["2663-337X"]},"month":"06","ddc":["530"],"title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7996","oa_version":"Published Version","file":[{"content_type":"application/x-zip-compressed","file_size":392794743,"creator":"dernst","file_name":"JK_thesis_latex_source_files.zip","access_level":"closed","date_updated":"2020-07-14T12:48:07Z","date_created":"2020-06-22T09:22:04Z","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","relation":"main_file","file_id":"7997"},{"access_level":"open_access","file_name":"PhD_thesis_JK_pdfa.pdf","content_type":"application/pdf","file_size":28453247,"creator":"dernst","relation":"main_file","file_id":"7998","checksum":"1de716bf110dbd77d383e479232bf496","date_created":"2020-06-22T09:21:29Z","date_updated":"2020-07-14T12:48:07Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.","lang":"eng"}],"page":"178","citation":{"apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996."},"date_published":"2020-06-22T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"22"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"_id":"8390","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","ddc":["000"],"oa_version":"Published Version","file":[{"file_name":"2020_Thesis_Royer.pdf","access_level":"open_access","creator":"dernst","file_size":30224591,"content_type":"application/pdf","file_id":"8391","relation":"main_file","date_created":"2020-09-14T13:39:14Z","date_updated":"2020-09-14T13:39:14Z","success":1,"checksum":"c914d2f88846032f3d8507734861b6ee"},{"file_name":"thesis_sources.zip","access_level":"closed","file_size":74227627,"content_type":"application/x-zip-compressed","creator":"dernst","relation":"main_file","file_id":"8392","date_updated":"2020-09-14T13:39:17Z","date_created":"2020-09-14T13:39:17Z","checksum":"ae98fb35d912cff84a89035ae5794d3c"}],"has_accepted_license":"1","article_processing_charge":"No","day":"14","citation":{"ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020."},"page":"197","date_published":"2020-09-14T00:00:00Z","file_date_updated":"2020-09-14T13:39:17Z","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ChLa"}],"publication_status":"published","related_material":{"record":[{"id":"7936","status":"public","relation":"part_of_dissertation"},{"id":"7937","relation":"part_of_dissertation","status":"public"},{"id":"8193","relation":"part_of_dissertation","status":"public"},{"id":"8092","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"911"}]},"author":[{"last_name":"Royer","first_name":"Amélie","orcid":"0000-0002-8407-0705","id":"3811D890-F248-11E8-B48F-1D18A9856A87","full_name":"Royer, Amélie"}],"date_created":"2020-09-14T13:42:09Z","date_updated":"2023-10-16T10:04:02Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"month":"09","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"doi":"10.15479/AT:ISTA:8390","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD"},{"abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"creator":"jtkadlec","file_size":21100497,"content_type":"application/zip","access_level":"closed","file_name":"thesis.zip","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-12T11:49:49Z","file_id":"7255","relation":"source_file"},{"file_name":"2020_Tkadlec_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":11670983,"creator":"dernst","relation":"main_file","file_id":"7367","date_created":"2020-01-28T07:32:42Z","date_updated":"2020-07-14T12:47:52Z","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985"}],"oa_version":"Published Version","ddc":["519"],"title":"A role of graphs in evolutionary processes","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7196","has_accepted_license":"1","article_processing_charge":"No","day":"12","date_published":"2020-01-12T00:00:00Z","page":"144","citation":{"chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196"},"file_date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-20T12:26:36Z","date_updated":"2023-10-17T12:29:46Z","related_material":{"record":[{"id":"7210","relation":"dissertation_contains","status":"public"},{"id":"5751","relation":"dissertation_contains","status":"public"},{"id":"7212","status":"public","relation":"dissertation_contains"}]},"author":[{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"}],"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","publication_identifier":{"eissn":["2663-337X"]},"month":"01","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7196","oa":1},{"has_accepted_license":"1","article_processing_charge":"No","day":"24","page":"119","citation":{"chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8156.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020.","ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156"},"date_published":"2020-07-24T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.","lang":"eng"}],"status":"public","title":"Topological methods in geometry and discrete mathematics","ddc":["514"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8156","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"source.zip","creator":"savvakum","file_size":1061740,"content_type":"application/zip","file_id":"8178","relation":"source_file","date_updated":"2020-07-27T12:44:51Z","date_created":"2020-07-27T12:44:51Z"},{"relation":"main_file","file_id":"8179","success":1,"date_updated":"2020-07-27T12:46:53Z","date_created":"2020-07-27T12:46:53Z","access_level":"open_access","file_name":"thesis_pdfa.pdf","content_type":"application/pdf","file_size":1336501,"creator":"savvakum"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8156","file_date_updated":"2020-07-27T12:46:53Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2020","date_updated":"2023-12-18T10:51:01Z","date_created":"2020-07-23T09:51:29Z","related_material":{"record":[{"id":"8182","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8183"},{"relation":"part_of_dissertation","status":"public","id":"8185"},{"id":"8184","status":"public","relation":"part_of_dissertation"},{"id":"6355","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"75"}]},"author":[{"first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey"}]},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-010-7"]},"month":"09","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"supervisor":[{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:8366","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"oa":1,"ec_funded":1,"file_date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-10T16:19:55Z","date_updated":"2024-02-21T12:44:29Z","related_material":{"record":[{"id":"7151","status":"deleted","relation":"research_data"},{"id":"7262","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8562"},{"id":"1001","relation":"part_of_dissertation","status":"public"},{"id":"8375","relation":"research_data","status":"public"}]},"author":[{"full_name":"Guseinov, Ruslan","last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","article_processing_charge":"No","has_accepted_license":"1","day":"21","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"date_published":"2020-09-21T00:00:00Z","page":"118","citation":{"ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366."},"abstract":[{"lang":"eng","text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_updated":"2020-09-10T16:11:49Z","date_created":"2020-09-10T16:11:49Z","checksum":"f8da89553da36037296b0a80f14ebf50","success":1,"relation":"main_file","file_id":"8367","content_type":"application/pdf","file_size":70950442,"creator":"rguseino","file_name":"thesis_rguseinov.pdf","access_level":"open_access"},{"access_level":"closed","file_name":"thesis_source.zip","file_size":76207597,"content_type":"application/x-zip-compressed","creator":"rguseino","relation":"source_file","file_id":"8374","checksum":"e8fd944c960c20e0e27e6548af69121d","date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-11T09:39:48Z"}],"title":"Computational design of curved thin shells: From glass façades to programmable matter","ddc":["000"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8366"}]