[{"supervisor":[{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"file":[{"creator":"jsteiner","content_type":"application/pdf","file_name":"Thesis_Julia_Steiner_pdfA.pdf","relation":"main_file","date_updated":"2021-09-16T12:40:56Z","access_level":"open_access","date_created":"2020-09-09T14:22:35Z","file_id":"8354","checksum":"2388d7e6e7a4d364c096fa89f305c3de","file_size":117547589},{"file_size":223328668,"checksum":"ba112f957b7145462d0ab79044873ee9","date_created":"2020-09-09T14:23:25Z","file_id":"8355","access_level":"closed","date_updated":"2020-09-15T08:48:37Z","file_name":"Thesis_Julia_Steiner.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jsteiner"}],"year":"2020","department":[{"_id":"LeSa"}],"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.","fulldoi":"https://doi.org/10.15479/AT:ISTA:8353","date_updated":"2026-04-08T07:23:36Z","day":"09","ddc":["572"],"type":"dissertation","has_accepted_license":"1","status":"public","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"page":"191","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"citation":{"apa":"Steiner, J. (2020). <i>Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>","mla":"Steiner, Julia. <i>Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>."},"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"status":"public","id":"8284","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"author":[{"id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0493-3775","first_name":"Julia","full_name":"Steiner, Julia","last_name":"Steiner"}],"file_date_updated":"2021-09-16T12:40:56Z","publication_identifier":{"issn":["2663-337X"]},"oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-09T14:27:01Z","doi":"10.15479/AT:ISTA:8353","_id":"8353","publisher":"Institute of Science and Technology Austria","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"month":"09","OA_place":"publisher","date_published":"2020-09-09T00:00:00Z","oa":1},{"author":[{"last_name":"Guseinov","full_name":"Guseinov, Ruslan","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"}],"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."}],"file_date_updated":"2020-09-16T15:11:01Z","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-010-7"]},"publication_status":"published","article_processing_charge":"No","doi":"10.15479/AT:ISTA:8366","date_created":"2020-09-10T16:19:55Z","citation":{"apa":"Guseinov, R. (2020). <i>Computational design of curved thin shells: From glass façades to programmable matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8366\">https://doi.org/10.15479/AT:ISTA:8366</a>","mla":"Guseinov, Ruslan. <i>Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8366\">10.15479/AT:ISTA:8366</a>.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8366\">10.15479/AT:ISTA:8366</a>","ieee":"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. <a href=\"https://doi.org/10.15479/AT:ISTA:8366\">https://doi.org/10.15479/AT:ISTA:8366</a>.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria."},"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8562"},{"status":"public","id":"8375","relation":"research_data"},{"id":"7151","status":"deleted","relation":"research_data"},{"relation":"part_of_dissertation","id":"1001","status":"public"},{"relation":"part_of_dissertation","id":"7262","status":"public"}]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"month":"09","OA_place":"publisher","date_published":"2020-09-21T00:00:00Z","oa":1,"_id":"8366","publisher":"Institute of Science and Technology Austria","title":"Computational design of curved thin shells: From glass façades to programmable matter","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.","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"supervisor":[{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd"}],"file":[{"file_size":70950442,"access_level":"open_access","file_id":"8367","date_created":"2020-09-10T16:11:49Z","checksum":"f8da89553da36037296b0a80f14ebf50","success":1,"content_type":"application/pdf","file_name":"thesis_rguseinov.pdf","relation":"main_file","creator":"rguseino","date_updated":"2020-09-10T16:11:49Z"},{"file_size":76207597,"access_level":"closed","file_id":"8374","date_created":"2020-09-11T09:39:48Z","checksum":"e8fd944c960c20e0e27e6548af69121d","date_updated":"2020-09-16T15:11:01Z","content_type":"application/x-zip-compressed","file_name":"thesis_source.zip","relation":"source_file","creator":"rguseino"}],"year":"2020","department":[{"_id":"BeBi"}],"type":"dissertation","has_accepted_license":"1","status":"public","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","ec_funded":1,"page":"118","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:8366","date_updated":"2026-04-08T07:25:22Z","day":"21","ddc":["000"]},{"main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392405","open_access":"1"}],"article_type":"original","title":"A model for soap film dynamics with evolving thickness","_id":"8384","publisher":"Association for Computing Machinery","volume":39,"month":"07","date_published":"2020-07-08T00:00:00Z","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19630"}]},"language":[{"iso":"eng"}],"intvolume":"        39","citation":{"apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., &#38; Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31."},"publication":"ACM Transactions on Graphics","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"oa_version":"Submitted Version","doi":"10.1145/3386569.3392405","date_created":"2020-09-13T22:01:18Z","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film."}],"author":[{"full_name":"Ishida, Sadashige","first_name":"Sadashige","orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida"},{"first_name":"Peter","full_name":"Synak, Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak"},{"first_name":"Fumiya","full_name":"Narita, Fumiya","last_name":"Narita"},{"first_name":"Toshiya","full_name":"Hachisuka, Toshiya","last_name":"Hachisuka"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"external_id":{"isi":["000583700300004"]},"article_number":"31","file_date_updated":"2020-11-23T09:03:19Z","scopus_import":"1","ddc":["000"],"fulldoi":"https://doi.org/10.1145/3386569.3392405","day":"08","date_updated":"2026-04-16T08:29:36Z","issue":"4","ec_funded":1,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"type":"journal_article","has_accepted_license":"1","status":"public","file":[{"date_updated":"2020-11-23T09:03:19Z","creator":"dernst","file_name":"2020_soapfilm_submitted.pdf","relation":"main_file","content_type":"application/pdf","success":1,"checksum":"813831ca91319d794d9748c276b24578","file_id":"8795","date_created":"2020-11-23T09:03:19Z","access_level":"open_access","file_size":14935529}],"year":"2020","department":[{"_id":"ChWo"}],"quality_controlled":"1","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176."},{"fulldoi":"https://doi.org/10.1145/3386569.3392412","day":"08","date_updated":"2026-04-16T08:31:55Z","scopus_import":"1","ddc":["000"],"type":"journal_article","has_accepted_license":"1","status":"public","ec_funded":1,"issue":"4","project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"file":[{"success":1,"file_size":38922662,"checksum":"cf4c1d361c3196c4bd424520a5588205","access_level":"open_access","file_id":"8794","date_created":"2020-11-23T09:01:22Z","date_updated":"2020-11-23T09:01:22Z","file_name":"2020_hylc_submitted.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst"}],"year":"2020","department":[{"_id":"ChWo"}],"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","quality_controlled":"1","_id":"8385","publisher":"Association for Computing Machinery","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392412"}],"article_type":"original","title":"Homogenized yarn-level cloth","acknowledged_ssus":[{"_id":"ScienComp"}],"month":"07","volume":39,"date_published":"2020-07-08T00:00:00Z","oa":1,"intvolume":"        39","citation":{"apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2020). Homogenized yarn-level cloth. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392412\">https://doi.org/10.1145/3386569.3392412</a>","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392412\">10.1145/3386569.3392412</a>.","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392412\">10.1145/3386569.3392412</a>","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392412\">https://doi.org/10.1145/3386569.3392412</a>."},"publication":"ACM Transactions on Graphics","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"related_material":{"record":[{"id":"12358","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"abstract":[{"text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver.","lang":"eng"}],"author":[{"last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Sperl, Georg"},{"last_name":"Narain","first_name":"Rahul","full_name":"Narain, Rahul"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"external_id":{"isi":["000583700300021"]},"article_number":"48","file_date_updated":"2020-11-23T09:01:22Z","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"oa_version":"Submitted Version","date_created":"2020-09-13T22:01:18Z","publication_status":"published","article_processing_charge":"No","doi":"10.1145/3386569.3392412"},{"citation":{"mla":"Royer, Amélie. <i>Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>.","apa":"Royer, A. (2020). <i>Leveraging structure in Computer Vision tasks for flexible Deep Learning models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8390\">10.15479/AT:ISTA:8390</a>","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8390\">https://doi.org/10.15479/AT:ISTA:8390</a>.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7936"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"status":"public","id":"911","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8193"},{"id":"7937","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"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. ","lang":"eng"}],"author":[{"last_name":"Royer","full_name":"Royer, Amélie","first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8407-0705"}],"file_date_updated":"2020-09-14T13:39:17Z","publication_identifier":{"isbn":["978-3-99078-007-7"],"issn":["2663-337X"]},"oa_version":"Published Version","publication_status":"published","doi":"10.15479/AT:ISTA:8390","article_processing_charge":"No","date_created":"2020-09-14T13:42:09Z","_id":"8390","publisher":"Institute of Science and Technology Austria","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"month":"09","oa":1,"date_published":"2020-09-14T00:00:00Z","OA_place":"publisher","year":"2020","supervisor":[{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"file":[{"file_id":"8391","date_created":"2020-09-14T13:39:14Z","access_level":"open_access","checksum":"c914d2f88846032f3d8507734861b6ee","file_size":30224591,"success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2020_Thesis_Royer.pdf","relation":"main_file","date_updated":"2020-09-14T13:39:14Z"},{"file_id":"8392","access_level":"closed","date_created":"2020-09-14T13:39:17Z","checksum":"ae98fb35d912cff84a89035ae5794d3c","file_size":74227627,"creator":"dernst","content_type":"application/x-zip-compressed","relation":"main_file","file_name":"thesis_sources.zip","date_updated":"2020-09-14T13:39:17Z"}],"department":[{"_id":"ChLa"}],"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.","day":"14","date_updated":"2026-04-08T07:26:44Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:8390","ddc":["000"],"type":"dissertation","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","status":"public","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","page":"197"},{"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","quality_controlled":"1","year":"2020","file":[{"date_updated":"2020-09-21T07:51:44Z","relation":"main_file","file_name":"2020_ACM_Skrivan.pdf","content_type":"application/pdf","creator":"dernst","success":1,"file_size":20223953,"checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","file_id":"8541","access_level":"open_access","date_created":"2020-09-21T07:51:44Z"}],"department":[{"_id":"ChWo"}],"type":"journal_article","status":"public","has_accepted_license":"1","project":[{"grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"issue":"4","day":"08","date_updated":"2026-04-16T08:26:38Z","fulldoi":"https://doi.org/10.1145/3386569.3392466","scopus_import":"1","ddc":["000"],"external_id":{"isi":["000583700300038"]},"abstract":[{"text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.","lang":"eng"}],"author":[{"full_name":"Skrivan, Tomas","first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan"},{"last_name":"Soderstrom","first_name":"Andreas","full_name":"Soderstrom, Andreas"},{"last_name":"Johansson","first_name":"John","full_name":"Johansson, John"},{"last_name":"Sprenger","full_name":"Sprenger, Christoph","first_name":"Christoph"},{"first_name":"Ken","full_name":"Museth, Ken","last_name":"Museth"},{"last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"file_date_updated":"2020-09-21T07:51:44Z","article_number":"65","oa_version":"Published Version","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"doi":"10.1145/3386569.3392466","date_created":"2020-09-20T22:01:37Z","publication_status":"published","article_processing_charge":"No","publication":"ACM Transactions on Graphics","citation":{"short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>.","mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>.","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &#38; Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>"},"intvolume":"        39","isi":1,"corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"07","volume":39,"oa":1,"date_published":"2020-07-08T00:00:00Z","_id":"8535","publisher":"Association for Computing Machinery","article_type":"original","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces"},{"corr_author":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/bend-dont-break/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"8761","status":"public","relation":"research_data"},{"status":"public","id":"8366","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"intvolume":"        39","citation":{"mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>","chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>.","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","ieee":"K. Gavriil <i>et al.</i>, “Computational design of cold bent glass façades,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6. Association for Computing Machinery, 2020.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. 2020;39(6). doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>"},"publication":"ACM Transactions on Graphics","oa_version":"Submitted Version","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"doi":"10.1145/3414685.3417843","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-23T11:30:02Z","author":[{"last_name":"Gavriil","first_name":"Konstantinos","full_name":"Gavriil, Konstantinos"},{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","first_name":"Ruslan","last_name":"Guseinov"},{"last_name":"Perez Rodriguez","first_name":"Jesus","full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pellis","full_name":"Pellis, Davide","first_name":"Davide"},{"orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425","full_name":"Henderson, Paul M","first_name":"Paul M","last_name":"Henderson"},{"last_name":"Rist","full_name":"Rist, Florian","first_name":"Florian"},{"full_name":"Pottmann, Helmut","first_name":"Helmut","last_name":"Pottmann"},{"last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface.","lang":"eng"}],"external_id":{"arxiv":["2009.03667"],"isi":["000595589100048"]},"article_number":"208","file_date_updated":"2023-05-23T20:54:43Z","article_type":"original","title":"Computational design of cold bent glass façades","_id":"8562","publisher":"Association for Computing Machinery","volume":39,"month":"11","date_published":"2020-11-26T00:00:00Z","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"creator":"bbickel","relation":"main_file","file_name":"coldglass.pdf","content_type":"application/pdf","date_updated":"2023-05-23T20:54:43Z","checksum":"c7f67717ad74e670b7daeae732abe151","file_id":"13084","access_level":"open_access","date_created":"2023-05-23T20:54:43Z","file_size":28964641,"success":1}],"year":"2020","department":[{"_id":"BeBi"}],"arxiv":1,"quality_controlled":"1","acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","scopus_import":"1","ddc":["000"],"fulldoi":"https://doi.org/10.1145/3414685.3417843","date_updated":"2026-04-08T07:25:22Z","day":"26","ec_funded":1,"issue":"6","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","has_accepted_license":"1","status":"public"},{"title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","article_type":"original","publisher":"Springer Nature","_id":"8581","date_published":"2020-11-01T00:00:00Z","volume":27,"month":"11","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/"}]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"citation":{"ama":"Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. <i>Nature Structural and Molecular Biology</i>. 2020;27(11):1077-1085. doi:<a href=\"https://doi.org/10.1038/s41594-020-0503-8\">10.1038/s41594-020-0503-8</a>","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","chicago":"Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41594-020-0503-8\">https://doi.org/10.1038/s41594-020-0503-8</a>.","ieee":"G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” <i>Nature Structural and Molecular Biology</i>, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020.","ista":"Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.","mla":"Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” <i>Nature Structural and Molecular Biology</i>, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:<a href=\"https://doi.org/10.1038/s41594-020-0503-8\">10.1038/s41594-020-0503-8</a>.","apa":"Pinke, G., Zhou, L., &#38; Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-020-0503-8\">https://doi.org/10.1038/s41594-020-0503-8</a>"},"intvolume":"        27","publication":"Nature Structural and Molecular Biology","article_processing_charge":"No","publication_status":"published","date_created":"2020-09-28T08:59:27Z","doi":"10.1038/s41594-020-0503-8","oa_version":"None","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"author":[{"id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","full_name":"Pinke, Gergely","last_name":"Pinke"},{"last_name":"Zhou","id":"3E751364-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1864-8951","full_name":"Zhou, Long","first_name":"Long"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"abstract":[{"text":"The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.","lang":"eng"}],"external_id":{"isi":["000569299400004"],"pmid":["32929284"]},"scopus_import":"1","pmid":1,"fulldoi":"https://doi.org/10.1038/s41594-020-0503-8","date_updated":"2025-07-10T11:57:09Z","day":"01","page":"1077-1085","issue":"11","status":"public","type":"journal_article","department":[{"_id":"LeSa"}],"year":"2020","quality_controlled":"1","acknowledgement":"We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission."},{"acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"date_published":"2020-07-12T00:00:00Z","volume":119,"month":"07","publisher":"ML Research Press","_id":"8724","title":"On the sample complexity of adversarial multi-source PAC learning","file_date_updated":"2021-02-15T09:00:01Z","external_id":{"arxiv":["2002.10384"]},"author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0009-5204-7621","full_name":"Konstantinov, Nikola H","first_name":"Nikola H","last_name":"Konstantinov"},{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias","first_name":"Elias","last_name":"Frantar"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. "}],"article_processing_charge":"No","publication_status":"published","date_created":"2020-11-05T15:25:58Z","oa_version":"Published Version","publication_identifier":{"issn":["2640-3498"]},"publication":"Proceedings of the 37th International Conference on Machine Learning","citation":{"short":"N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425.","ama":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ML Research Press; 2020:5416-5425.","ieee":"N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Online, 2020, vol. 119, pp. 5416–5425.","chicago":"Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:5416–25. ML Research Press, 2020.","ista":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.","mla":"Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, ML Research Press, 2020, pp. 5416–25.","apa":"Konstantinov, N. H., Frantar, E., Alistarh, D.-A., &#38; Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 5416–5425). Online: ML Research Press."},"intvolume":"       119","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"supplementary_material","url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf"}],"record":[{"id":"10799","status":"public","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","status":"public","has_accepted_license":"1","type":"conference","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"page":"5416-5425","ec_funded":1,"date_updated":"2026-04-07T14:19:48Z","day":"12","ddc":["000"],"scopus_import":"1","acknowledgement":"Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","quality_controlled":"1","conference":{"end_date":"2020-07-18","location":"Online","name":"ICML: International Conference on Machine Learning","start_date":"2020-07-12"},"arxiv":1,"department":[{"_id":"DaAl"},{"_id":"ChLa"}],"year":"2020","file":[{"date_updated":"2021-02-15T09:00:01Z","file_name":"2020_PMLR_Konstantinov.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","success":1,"file_size":281286,"checksum":"cc755d0054bc4b2be778ea7aa7884d2f","file_id":"9120","date_created":"2021-02-15T09:00:01Z","access_level":"open_access"}]},{"oa_version":"Published Version","date_created":"2020-11-16T10:47:18Z","article_processing_charge":"No","doi":"10.15479/AT:ISTA:8761","author":[{"last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","full_name":"Guseinov, Ruslan"}],"file_date_updated":"2020-11-18T10:04:59Z","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://github.com/russelmann/cold-glass-acm","relation":"software"}],"record":[{"id":"8562","status":"public","relation":"used_in_publication"}]},"citation":{"mla":"Guseinov, Ruslan. <i>Supplementary Data for “Computational Design of Cold Bent Glass Façades.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>.","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>","short":"R. Guseinov, (2020)."},"month":"11","date_published":"2020-11-23T00:00:00Z","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Supplementary data for \"Computational design of cold bent glass façades\"","_id":"8761","publisher":"Institute of Science and Technology Austria","file":[{"creator":"rguseino","file_name":"mdn_model.tar.gz","relation":"main_file","content_type":"application/x-gzip","date_updated":"2020-11-16T10:31:29Z","checksum":"f5ae57b97017b9f61081032703361233","access_level":"open_access","date_created":"2020-11-16T10:31:29Z","file_id":"8762","file_size":15378270,"success":1},{"success":1,"access_level":"open_access","file_id":"8763","date_created":"2020-11-16T10:43:23Z","checksum":"b0d25e04060ee78c585ee2f23542c744","file_size":615387734,"date_updated":"2020-11-16T10:43:23Z","creator":"rguseino","content_type":"application/x-gzip","relation":"main_file","file_name":"optimal_panels_data.tar.gz"},{"success":1,"file_size":1228,"checksum":"69c1dde3434ada86d125e0c2588caf1e","access_level":"open_access","file_id":"8770","date_created":"2020-11-18T10:04:59Z","date_updated":"2020-11-18T10:04:59Z","relation":"main_file","file_name":"readme.txt","content_type":"text/plain","creator":"rguseino"}],"year":"2020","department":[{"_id":"BeBi"}],"ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"license":"https://creativecommons.org/licenses/by/4.0/","type":"research_data","has_accepted_license":"1","status":"public","ddc":["000"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:8761","contributor":[{"contributor_type":"researcher","last_name":"Gavriil","first_name":"Konstantinos"},{"orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","contributor_type":"researcher","last_name":"Guseinov"},{"first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","contributor_type":"researcher"},{"first_name":"Davide","last_name":"Pellis","contributor_type":"researcher"},{"last_name":"Henderson","contributor_type":"researcher","first_name":"Paul M","orcid":"0000-0002-5198-7445","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Florian","last_name":"Rist","contributor_type":"researcher"},{"last_name":"Pottmann","contributor_type":"researcher","first_name":"Helmut"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","contributor_type":"researcher","last_name":"Bickel"}],"date_updated":"2025-04-15T07:16:12Z","day":"23"},{"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","quality_controlled":"1","keyword":["Computer Networks and Communications"],"year":"2020","file":[{"file_size":38969122,"checksum":"7605f605acd84d0942b48bc7a1c2d72e","access_level":"open_access","date_created":"2020-11-23T09:05:13Z","file_id":"8796","success":1,"relation":"main_file","file_name":"2020_poff_revisited.pdf","content_type":"application/pdf","creator":"dernst","date_updated":"2020-11-23T09:05:13Z"}],"department":[{"_id":"ChWo"}],"type":"journal_article","status":"public","has_accepted_license":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"issue":"2","ec_funded":1,"page":"89-99","date_updated":"2024-10-22T09:58:14Z","day":"01","fulldoi":"https://doi.org/10.1111/cgf.13914","scopus_import":"1","ddc":["000"],"external_id":{"isi":["000548709600008"]},"abstract":[{"text":"This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate.","lang":"eng"}],"author":[{"first_name":"Camille","full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan"}],"file_date_updated":"2020-11-23T09:05:13Z","oa_version":"Submitted Version","publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"article_processing_charge":"No","date_created":"2020-11-17T09:35:10Z","doi":"10.1111/cgf.13914","publication_status":"published","publication":"Computer Graphics Forum","intvolume":"        39","citation":{"ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. 2020;39(2):89-99. doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>.","ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” <i>Computer Graphics Forum</i>, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","apa":"Schreck, C., &#38; Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>","mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>."},"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"volume":39,"month":"05","oa":1,"date_published":"2020-05-01T00:00:00Z","_id":"8765","publisher":"Wiley","article_type":"original","title":"A practical method for animating anisotropic elastoplastic materials"},{"file":[{"file_size":3958727,"file_id":"8975","date_created":"2020-12-28T08:16:10Z","access_level":"open_access","checksum":"55d43ea0061cc4027ba45e966e1db8cc","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2020_NatureComm_Faessler.pdf","creator":"dernst","date_updated":"2020-12-28T08:16:10Z"}],"year":"2020","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"quality_controlled":"1","fulldoi":"https://doi.org/10.1038/s41467-020-20286-x","day":"22","date_updated":"2025-04-15T07:52:12Z","scopus_import":"1","ddc":["570"],"type":"journal_article","has_accepted_license":"1","status":"public","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020)."},"intvolume":"        11","publication":"Nature Communications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","corr_author":"1","isi":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage"}]},"language":[{"iso":"eng"}],"author":[{"first_name":"Florian","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler"},{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev"},{"orcid":"0000-0003-3904-947X","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"external_id":{"isi":["000603078000003"]},"article_number":"6437","file_date_updated":"2020-12-28T08:16:10Z","oa_version":"Published Version","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","date_created":"2020-12-23T08:25:45Z","article_processing_charge":"No","doi":"10.1038/s41467-020-20286-x","_id":"8971","publisher":"Springer Nature","article_type":"original","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"month":"12","date_published":"2020-12-22T00:00:00Z","oa":1},{"type":"journal_article","has_accepted_license":"1","status":"public","issue":"1","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF"}],"fulldoi":"https://doi.org/10.1371/journal.ppat.1008277","pmid":1,"day":"27","date_updated":"2025-04-15T08:24:51Z","scopus_import":"1","ddc":["570"],"quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:47:59Z","relation":"main_file","file_name":"2020_PLOSPatho_Dick.pdf","content_type":"application/pdf","creator":"dernst","file_size":4551246,"checksum":"a297f54d1fef0efe4789ca00f37f241e","access_level":"open_access","file_id":"7484","date_created":"2020-02-11T10:07:28Z"}],"year":"2020","department":[{"_id":"FlSc"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":16,"month":"01","date_published":"2020-01-27T00:00:00Z","oa":1,"_id":"7464","publisher":"Public Library of Science","article_type":"original","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","author":[{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"last_name":"Xu","full_name":"Xu, Chaoyi","first_name":"Chaoyi"},{"first_name":"Dustin R.","full_name":"Morado, Dustin R.","last_name":"Morado"},{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9523-9089","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk"},{"first_name":"Clifton L.","full_name":"Ricana, Clifton L.","last_name":"Ricana"},{"full_name":"Lyddon, Terri D.","first_name":"Terri D.","last_name":"Lyddon"},{"first_name":"Arianna M.","full_name":"Broad, Arianna M.","last_name":"Broad"},{"first_name":"J. Ryan","full_name":"Feathers, J. Ryan","last_name":"Feathers"},{"last_name":"Johnson","full_name":"Johnson, Marc C.","first_name":"Marc C."},{"last_name":"Vogt","first_name":"Volker M.","full_name":"Vogt, Volker M."},{"last_name":"Perilla","full_name":"Perilla, Juan R.","first_name":"Juan R."},{"last_name":"Briggs","full_name":"Briggs, John A. G.","first_name":"John A. G."},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur"}],"abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"article_number":"e1008277","file_date_updated":"2020-07-14T12:47:59Z","publication_identifier":{"issn":["1553-7374"]},"oa_version":"Published Version","date_created":"2020-02-06T18:47:17Z","doi":"10.1371/journal.ppat.1008277","publication_status":"published","article_processing_charge":"No","intvolume":"        16","citation":{"mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020.","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020)."},"publication":"PLOS Pathogens","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"related_material":{"record":[{"relation":"research_data","id":"9723","status":"deleted"}]},"language":[{"iso":"eng"}]},{"publication":"Journal of Structural Biology","intvolume":"       212","citation":{"apa":"Fäßler, F., Zens, B., Hauschild, R., &#38; Schur, F. K. (2020). 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>","mla":"Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>, vol. 212, no. 3, 107633, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (2020).","ama":"Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. <i>Journal of Structural Biology</i>. 2020;212(3). doi:<a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">10.1016/j.jsb.2020.107633</a>","ieee":"F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy,” <i>Journal of Structural Biology</i>, vol. 212, no. 3. Elsevier, 2020.","chicago":"Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur. “3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” <i>Journal of Structural Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jsb.2020.107633\">https://doi.org/10.1016/j.jsb.2020.107633</a>.","ista":"Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Journal of Structural Biology. 212(3), 107633."},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14592"},{"relation":"dissertation_contains","status":"public","id":"12491"}]},"external_id":{"pmid":["32987119"],"isi":["000600997800008"]},"author":[{"last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","full_name":"Fäßler, Florian"},{"last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","first_name":"Bettina","full_name":"Zens, Bettina"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM"}],"abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"file_date_updated":"2020-12-10T14:01:10Z","article_number":"107633","oa_version":"Published Version","publication_identifier":{"issn":["1047-8477"]},"date_created":"2020-09-29T13:24:06Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.jsb.2020.107633","_id":"8586","publisher":"Elsevier","article_type":"original","title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"12","volume":212,"oa":1,"date_published":"2020-12-01T00:00:00Z","year":"2020","file":[{"success":1,"file_size":7076870,"date_created":"2020-12-10T14:01:10Z","file_id":"8937","access_level":"open_access","checksum":"c48cbf594e84fc2f91966ffaafc0918c","date_updated":"2020-12-10T14:01:10Z","content_type":"application/pdf","relation":"main_file","file_name":"2020_JourStrucBiology_Faessler.pdf","creator":"dernst"}],"department":[{"_id":"FlSc"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF, P33367) to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF) and the Electron Microscopy Facility (EMF). We thank Georgi Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing our grid holders in different experimental setups and Daniel Gütl and the Kondrashov group (IST Austria) for granting us repeated access to their 3D printers. We also thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science) for illustrating the graphical abstract.","quality_controlled":"1","keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"day":"01","date_updated":"2026-10-16T22:30:03Z","pmid":1,"fulldoi":"https://doi.org/10.1016/j.jsb.2020.107633","scopus_import":"1","ddc":["570"],"type":"journal_article","status":"public","has_accepted_license":"1","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"issue":"3"},{"citation":{"ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>."},"intvolume":"        11","publication":"Genome biology and evolution","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"related_material":{"record":[{"relation":"popular_science","id":"6060","status":"public"}]},"language":[{"iso":"eng"}],"author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","full_name":"Huylmans, Ann K","last_name":"Huylmans"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","full_name":"Toups, Melissa A","last_name":"Toups"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"last_name":"Gammerdinger","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J","first_name":"William J"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.","lang":"eng"}],"external_id":{"isi":["000476569800003"]},"file_date_updated":"2020-07-14T12:47:29Z","oa_version":"Published Version","publication_identifier":{"eissn":["1759-6653"]},"publication_status":"published","doi":"10.1093/gbe/evz053","date_created":"2019-05-13T07:58:38Z","article_processing_charge":"No","_id":"6418","publisher":"Oxford University Press","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"month":"04","date_published":"2019-04-01T00:00:00Z","oa":1,"file":[{"file_name":"2019_GBE_Huylmans.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","file_size":1256303,"checksum":"7d0ede297b6741f3dc89cd59017c7642","file_id":"6446","date_created":"2019-05-14T08:29:38Z","access_level":"open_access"}],"year":"2019","department":[{"_id":"BeVi"}],"quality_controlled":"1","fulldoi":"https://doi.org/10.1093/gbe/evz053","date_updated":"2025-04-14T07:41:21Z","day":"01","scopus_import":"1","ddc":["570"],"type":"journal_article","has_accepted_license":"1","status":"public","page":"1033-1044","ec_funded":1,"issue":"4","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","call_identifier":"H2020"}]},{"quality_controlled":"1","department":[{"_id":"ChWo"}],"year":"2019","file":[{"file_id":"6443","access_level":"open_access","date_created":"2019-05-14T07:03:55Z","checksum":"1b737dfe3e051aba8f3f4ab1dceda673","file_size":44328918,"date_updated":"2020-07-14T12:47:30Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2019_ACM_Schreck.pdf"}],"project":[{"call_identifier":"H2020","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"issue":"4","ec_funded":1,"status":"public","has_accepted_license":"1","type":"journal_article","ddc":["000","005"],"scopus_import":"1","day":"01","date_updated":"2024-10-22T09:58:22Z","fulldoi":"https://doi.org/10.1145/3306346.3323002","doi":"10.1145/3306346.3323002","publication_status":"published","date_created":"2019-05-14T07:04:06Z","article_processing_charge":"No","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:47:30Z","article_number":"130","external_id":{"isi":["000475740600104"]},"author":[{"full_name":"Schreck, Camille","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck"},{"last_name":"Hafner","first_name":"Christian","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"abstract":[{"lang":"eng","text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples."}],"language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/"}]},"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"ACM Transactions on Graphics","intvolume":"        38","citation":{"mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 130, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>.","apa":"Schreck, C., Hafner, C., &#38; Wojtan, C. (2019). Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>.","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130."},"oa":1,"date_published":"2019-07-01T00:00:00Z","month":"07","volume":38,"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Fundamental solutions for water wave animation","publisher":"ACM","_id":"6442"},{"department":[{"_id":"LeSa"}],"year":"2019","quality_controlled":"1","scopus_import":"1","fulldoi":"https://doi.org/10.1126/science.aaw9144","pmid":1,"day":"23","date_updated":"2023-08-29T07:52:02Z","issue":"6455","status":"public","type":"journal_article","related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/"}]},"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"citation":{"chicago":"Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” <i>Science</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/science.aaw9144\">https://doi.org/10.1126/science.aaw9144</a>.","ieee":"L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase,” <i>Science</i>, vol. 365, no. 6455. AAAS, 2019.","ista":"Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144.","short":"L. Zhou, L.A. Sazanov, Science 365 (2019).","ama":"Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. <i>Science</i>. 2019;365(6455). doi:<a href=\"https://doi.org/10.1126/science.aaw9144\">10.1126/science.aaw9144</a>","mla":"Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” <i>Science</i>, vol. 365, no. 6455, eaaw9144, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/science.aaw9144\">10.1126/science.aaw9144</a>.","apa":"Zhou, L., &#38; Sazanov, L. A. (2019). Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aaw9144\">https://doi.org/10.1126/science.aaw9144</a>"},"intvolume":"       365","publication":"Science","article_processing_charge":"No","publication_status":"published","date_created":"2019-09-07T19:04:45Z","doi":"10.1126/science.aaw9144","oa_version":"None","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_number":"eaaw9144","author":[{"last_name":"Zhou","orcid":"0000-0002-1864-8951","id":"3E751364-F248-11E8-B48F-1D18A9856A87","first_name":"Long","full_name":"Zhou, Long"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"abstract":[{"text":"V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation across theplasma membrane using the rotary-catalysis mechanism. They belong to the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthasesin overall architecture. We solved cryo–electron microscopy structures of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs, in three rotationalstates and two substates. These structures indicate substantial flexibility betweenV1and Voin a working enzyme, which results from mechanical competition between centralshaft rotation and resistance from the peripheral stalks. We also describedetails of adenosine diphosphate inhibition release, V1-Votorque transmission, andproton translocation, which are relevant for the entire V-type ATPase family.","lang":"eng"}],"external_id":{"pmid":["31439765"],"isi":["000482464000043"]},"title":"Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase","publisher":"AAAS","_id":"6859","date_published":"2019-08-23T00:00:00Z","month":"08","volume":365,"acknowledged_ssus":[{"_id":"ScienComp"}]},{"month":"10","volume":4,"oa":1,"date_published":"2019-10-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02211"}],"title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","_id":"6978","publisher":"American Physical Society","oa_version":"Preprint","date_created":"2019-11-04T10:04:01Z","publication_status":"published","doi":"10.1103/PhysRevFluids.4.102401","article_processing_charge":"No","external_id":{"isi":["000493510400001"],"arxiv":["1810.02211"]},"abstract":[{"text":"In  pipes  and  channels,  the  onset  of  turbulence  is  initially  dominated  by  localizedtransients,  which  lead  to  sustained  turbulence  through  their  collective  dynamics.  In  thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating  laminar  and  turbulent  flow,  we  identify  transverse  homoclinic  orbits,  thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.","lang":"eng"}],"author":[{"last_name":"Budanur","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"},{"first_name":"Akshunna","full_name":"Dogra, Akshunna","last_name":"Dogra"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"publication":"Physical Review Fluids","intvolume":"         4","citation":{"ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” <i>Physical Review Fluids</i>, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” <i>Physical Review Fluids</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">https://doi.org/10.1103/PhysRevFluids.4.102401</a>.","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.","ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. <i>Physical Review Fluids</i>. 2019;4(10):102401. doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">10.1103/PhysRevFluids.4.102401</a>","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” <i>Physical Review Fluids</i>, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">10.1103/PhysRevFluids.4.102401</a>.","apa":"Budanur, N. B., Dogra, A., &#38; Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">https://doi.org/10.1103/PhysRevFluids.4.102401</a>"},"page":"102401","issue":"10","type":"journal_article","status":"public","scopus_import":"1","day":"01","date_updated":"2023-08-30T07:20:03Z","fulldoi":"https://doi.org/10.1103/PhysRevFluids.4.102401","quality_controlled":"1","year":"2019","department":[{"_id":"BjHo"}],"arxiv":1},{"day":"07","date_updated":"2026-04-08T14:02:12Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:6435","ddc":["570","006","578","592"],"status":"public","has_accepted_license":"1","type":"dissertation","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"ec_funded":1,"page":"183","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","department":[{"_id":"SyCr"}],"year":"2019","supervisor":[{"full_name":"Cremer, Sylvia M","first_name":"Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"file":[{"embargo":"2020-05-08","date_updated":"2021-02-11T11:17:15Z","content_type":"application/pdf","file_name":"tesisDoctoradoBC.pdf","relation":"main_file","creator":"casillas","file_size":3895187,"file_id":"6438","date_created":"2019-05-13T09:16:20Z","access_level":"open_access","checksum":"6daf2d2086111aa8fd3fbc919a3e2833"},{"date_updated":"2020-07-14T12:47:30Z","relation":"source_file","file_name":"tesisDoctoradoBC.zip","content_type":"application/zip","creator":"casillas","file_size":7365118,"embargo_to":"open_access","checksum":"3d221aaff7559a7060230a1ff610594f","access_level":"closed","file_id":"6439","date_created":"2019-05-13T09:16:20Z"}],"keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"publisher":"Institute of Science and Technology Austria","_id":"6435","title":"Collective defenses of garden ants against a fungal pathogen","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"oa":1,"OA_place":"publisher","date_published":"2019-05-07T00:00:00Z","month":"05","citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>"},"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"1999","relation":"part_of_dissertation"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","file_date_updated":"2021-02-11T11:17:15Z","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","last_name":"Casillas Perez"}],"publication_status":"published","article_processing_charge":"No","date_created":"2019-05-13T08:58:35Z","doi":"10.15479/AT:ISTA:6435","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]}},{"oa":1,"date_published":"2019-09-12T00:00:00Z","volume":573,"month":"09","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","article_type":"letter_note","publisher":"Springer Nature","_id":"6848","publication_status":"published","date_created":"2019-09-04T06:21:41Z","doi":"10.1038/s41586-019-1519-2","article_processing_charge":"No","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"oa_version":"Submitted Version","file_date_updated":"2020-11-26T16:33:44Z","external_id":{"isi":["000485415400061"],"pmid":["31462775"]},"abstract":[{"lang":"eng","text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9."}],"author":[{"first_name":"Domen","full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6018-3422","last_name":"Kampjut"},{"last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8340"}]},"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature","citation":{"apa":"Kampjut, D., &#38; Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>.","ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. 2019;573(7773):291–295. doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” <i>Nature</i>, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>."},"intvolume":"       573","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"ec_funded":1,"page":"291–295","issue":"7773","status":"public","has_accepted_license":"1","type":"journal_article","ddc":["572"],"scopus_import":"1","date_updated":"2026-10-16T22:30:51Z","day":"12","fulldoi":"https://doi.org/10.1038/s41586-019-1519-2","pmid":1,"quality_controlled":"1","acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","department":[{"_id":"LeSa"}],"year":"2019","file":[{"success":1,"file_size":3066206,"checksum":"52728cda5210a3e9b74cc204e8aed3d5","file_id":"8821","date_created":"2020-11-26T16:33:44Z","access_level":"open_access","date_updated":"2020-11-26T16:33:44Z","file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf","relation":"main_file","content_type":"application/pdf","creator":"lsazanov"}]}]