[{"ec_funded":1,"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_PDFA.pdf","date_updated":"2020-07-14T12:48:01Z","file_size":3297129,"creator":"dernst"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","file_id":"7658","file_size":1063908,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"Thesis_Forkert_source.zip","date_created":"2020-04-14T10:47:59Z"}],"alternative_title":["ISTA Thesis"],"month":"03","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."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:01Z","department":[{"_id":"JaMa"}],"date_updated":"2023-09-07T13:03:12Z","supervisor":[{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"ddc":["510"],"type":"dissertation","status":"public","_id":"7629","page":"154","date_created":"2020-04-02T06:40:23Z","doi":"10.15479/AT:ISTA:7629","date_published":"2020-03-31T00:00:00Z","year":"2020","has_accepted_license":"1","day":"31","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","full_name":"Forkert, Dominik L","last_name":"Forkert"}],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","citation":{"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.","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629","apa":"Forkert, D. L. (2020). Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}]},{"page":"158","doi":"10.15479/AT:ISTA:8574","date_published":"2020-09-20T00:00:00Z","date_created":"2020-09-28T07:33:38Z","has_accepted_license":"1","year":"2020","day":"20","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"}],"article_processing_charge":"No","title":"Local adaptation in metapopulations","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574","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.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"dernst","date_updated":"2020-09-28T07:25:35Z","file_size":6354833,"date_created":"2020-09-28T07:25:35Z","file_name":"thesis_EnikoSzep_final.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","success":1},{"file_size":23020401,"date_updated":"2020-09-28T07:25:37Z","creator":"dernst","file_name":"thesisFiles_EnikoSzep.zip","date_created":"2020-09-28T07:25:37Z","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"8576","checksum":"a8de2c14a1bb4e53c857787efbb289e1"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","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"}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"file_date_updated":"2020-09-28T07:25:37Z","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"date_updated":"2023-09-07T13:11:39Z","ddc":["570"],"type":"dissertation","status":"public","_id":"8574"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria.","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.","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","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","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:10.15479/AT:ISTA:7514"},"title":"The free energy of a dilute two-dimensional Bose gas","article_processing_charge":"No","author":[{"full_name":"Mayer, Simon","last_name":"Mayer","first_name":"Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"24","year":"2020","has_accepted_license":"1","date_created":"2020-02-24T09:17:27Z","doi":"10.15479/AT:ISTA:7514","date_published":"2020-02-24T00:00:00Z","page":"148","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["510"],"date_updated":"2023-09-07T13:12:42Z","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"department":[{"_id":"RoSe"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:59Z","_id":"7514","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:59Z","file_size":1563429,"creator":"dernst","date_created":"2020-02-24T09:15:06Z","file_name":"thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","file_id":"7515"},{"date_created":"2020-02-24T09:15:16Z","file_name":"thesis_source.zip","creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":2028038,"checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_id":"7516","access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7524"}]},"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"02","alternative_title":["ISTA Thesis"]},{"doi":"10.15479/AT:ISTA:8353","date_published":"2020-09-09T00:00:00Z","date_created":"2020-09-09T14:27:01Z","page":"191","day":"09","has_accepted_license":"1","year":"2020","publisher":"Institute of Science and Technology Austria","oa":1,"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.","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","author":[{"first_name":"Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775","full_name":"Steiner, Julia","last_name":"Steiner"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","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","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:10.15479/AT:ISTA:8353","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.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","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."},"project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"related_material":{"record":[{"id":"8284","status":"public","relation":"part_of_dissertation"}]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8354","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","file_size":117547589,"creator":"jsteiner","date_created":"2020-09-09T14:22:35Z","file_name":"Thesis_Julia_Steiner_pdfA.pdf"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"8355","checksum":"ba112f957b7145462d0ab79044873ee9","date_updated":"2020-09-15T08:48:37Z","file_size":223328668,"creator":"jsteiner","date_created":"2020-09-09T14:23:25Z","file_name":"Thesis_Julia_Steiner.docx"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"None","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"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"file_date_updated":"2021-09-16T12:40:56Z","department":[{"_id":"LeSa"}],"ddc":["572"],"supervisor":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"date_updated":"2023-09-07T13:14:09Z","status":"public","type":"dissertation","_id":"8353"},{"_id":"8589","status":"public","type":"dissertation","ddc":["580"],"date_updated":"2023-09-07T13:13:05Z","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"file_date_updated":"2021-10-01T13:33:02Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8590","checksum":"c4bda1947d4c09c428ac9ce667b02327","creator":"dernst","file_size":49198118,"date_updated":"2020-09-30T14:50:20Z","file_name":"2020_Han_Thesis.docx","date_created":"2020-09-30T14:50:20Z"},{"checksum":"3f4f5d1718c2230adf30639ecaf8a00b","file_id":"8591","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_Han_Thesis.pdf","date_created":"2020-09-30T14:49:59Z","file_size":15513963,"date_updated":"2021-10-01T13:33:02Z","creator":"dernst"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"7643","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:10.15479/AT:ISTA:8589","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020.","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.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria."},"title":"Novel insights into PIN polarity regulation during Arabidopsis development","article_processing_charge":"No","author":[{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"}],"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.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"30","year":"2020","has_accepted_license":"1","date_created":"2020-09-30T14:50:51Z","date_published":"2020-09-30T00:00:00Z","doi":"10.15479/AT:ISTA:8589","page":"164"},{"acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"24","year":"2020","has_accepted_license":"1","date_created":"2020-07-23T09:51:28Z","doi":"10.15479/AT:ISTA:8155","date_published":"2020-07-24T00:00:00Z","page":"310","project":[{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","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.","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","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","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."},"title":"Gene regulation across scales – how biophysical constraints shape evolution","article_processing_charge":"No","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"}],"oa_version":"Published Version","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"}],"month":"07","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8176","success":1,"date_updated":"2020-07-27T12:00:07Z","file_size":16638998,"creator":"rgrah","date_created":"2020-07-27T12:00:07Z","file_name":"Thesis_RokGrah_200727_convertedNew.pdf"},{"file_id":"8177","content_type":"application/zip","access_level":"closed","relation":"main_file","date_created":"2020-07-27T12:02:23Z","file_name":"Thesis_new.zip","date_updated":"2020-07-30T13:04:55Z","file_size":347459978,"creator":"rgrah"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7675"},{"relation":"part_of_dissertation","id":"7569","status":"public"},{"id":"7652","status":"public","relation":"part_of_dissertation"}]},"_id":"8155","status":"public","type":"dissertation","ddc":["530","570"],"date_updated":"2023-09-07T13:13:27Z","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-30T13:04:55Z"},{"ddc":["514"],"date_updated":"2023-09-07T13:15:30Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"department":[{"_id":"HeEd"},{"_id":"GradSch"}],"file_date_updated":"2020-07-14T12:47:58Z","_id":"7460","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_id":"7461","checksum":"1df9f8c530b443c0e63a3f2e4fde412e","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-06T14:43:54Z","file_name":"thesis_ist-final_noack.pdf","date_updated":"2020-07-14T12:47:58Z","file_size":76195184,"creator":"koelsboe"},{"creator":"koelsboe","file_size":122103715,"date_updated":"2020-07-14T12:47:58Z","file_name":"latex-files.zip","date_created":"2020-02-06T14:52:45Z","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","description":"latex source files, figures","file_id":"7462","checksum":"7a52383c812b0be64d3826546509e5a4"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"6608","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","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."}],"month":"02","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7460.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","mla":"Ölsböck, Katharina. The Hole System of Triangulated Shapes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7460.","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:10.15479/AT:ISTA:7460","apa":"Ölsböck, K. (2020). The hole system of triangulated shapes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7460","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020."},"title":"The hole system of triangulated shapes","article_processing_charge":"No","author":[{"last_name":"Ölsböck","full_name":"Ölsböck, Katharina","orcid":"0000-0002-4672-8297","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87"}],"day":"10","year":"2020","has_accepted_license":"1","date_created":"2020-02-06T14:56:53Z","date_published":"2020-02-10T00:00:00Z","doi":"10.15479/AT:ISTA:7460","page":"155","oa":1,"publisher":"Institute of Science and Technology Austria"},{"related_material":{"record":[{"status":"public","id":"6677","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"7897","checksum":"b39e2e1c376f5819b823fb7077491c64","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_Thesis_Kamath.pdf","date_created":"2020-05-26T14:08:13Z","file_size":1622742,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst"},{"file_size":15301529,"date_updated":"2020-07-14T12:48:04Z","creator":"dernst","file_name":"Thesis_Kamath.zip","date_created":"2020-05-26T14:08:23Z","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"7898","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"05","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"}],"oa_version":"Published Version","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:04Z","supervisor":[{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_updated":"2023-09-07T13:15:55Z","ddc":["000"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7896","page":"126","date_published":"2020-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:7896","date_created":"2020-05-26T14:08:55Z","has_accepted_license":"1","year":"2020","day":"25","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"}],"article_processing_charge":"No","title":"On the average-case hardness of total search problems","citation":{"ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","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.","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","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi: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.","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}]},{"department":[{"_id":"HeEd"},{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:05Z","ddc":["516","514"],"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"date_updated":"2023-09-07T13:17:37Z","status":"public","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"type":"dissertation","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"_id":"7944","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7950"},{"relation":"part_of_dissertation","status":"public","id":"5986"}]},"file":[{"creator":"zmasarov","date_updated":"2020-07-14T12:48:05Z","file_size":13661779,"date_created":"2020-06-08T00:34:00Z","file_name":"THESIS_Zuzka_Masarova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","file_id":"7945"},{"creator":"zmasarov","file_size":32184006,"date_updated":"2020-07-14T12:48:05Z","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","date_created":"2020-06-08T00:35:30Z","relation":"source_file","access_level":"closed","content_type":"application/zip","checksum":"45341a35b8f5529c74010b7af43ac188","file_id":"7946"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-005-3"]},"degree_awarded":"PhD","publication_status":"published","month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars."}],"title":"Reconfiguration problems","author":[{"first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7944.","ama":"Masárová Z. Reconfiguration problems. 2020. doi:10.15479/AT:ISTA:7944","apa":"Masárová, Z. (2020). Reconfiguration problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7944","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","mla":"Masárová, Zuzana. Reconfiguration Problems. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7944."},"date_published":"2020-06-09T00:00:00Z","doi":"10.15479/AT:ISTA:7944","date_created":"2020-06-08T00:49:46Z","page":"160","day":"09","has_accepted_license":"1","year":"2020","publisher":"Institute of Science and Technology Austria","oa":1},{"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2020-09-08T09:00:29Z","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","date_updated":"2021-09-16T12:49:12Z","file_size":65246782,"creator":"dernst","checksum":"70871b335a595252a66c6bbf0824fb02","file_id":"8342","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"59a62275088b00b7241e6ff4136434c7","file_id":"8343","file_size":31259058,"date_updated":"2021-09-16T12:49:12Z","creator":"dernst","file_name":"2020_Urban_Bezeljak_Thesis.pdf","date_created":"2020-09-08T09:00:27Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7580","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","supervisor":[{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:17:06Z","ddc":["570"],"file_date_updated":"2021-09-16T12:49:12Z","department":[{"_id":"MaLo"}],"_id":"8341","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","has_accepted_license":"1","year":"2020","day":"08","page":"215","doi":"10.15479/AT:ISTA:8341","date_published":"2020-09-08T00:00:00Z","date_created":"2020-09-08T08:53:53Z","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.","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","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","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","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.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Bezeljak","orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban"}],"article_processing_charge":"No","title":"In vitro reconstitution of a Rab activation switch"}]