[{"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/"}],"record":[{"status":"public","relation":"software","id":"9327"},{"relation":"dissertation_contains","id":"12358","status":"public"}]},"isi":1,"main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"issue":"4","language":[{"iso":"eng"}],"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 Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. 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.","external_id":{"isi":["000674930900132"]},"date_updated":"2026-06-18T19:57:47Z","date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459816","year":"2021","day":"01","author":[{"full_name":"Sperl, Georg","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"publication_status":"published","citation":{"ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168.","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>."},"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"title":"Mechanics-aware deformation of yarn pattern geometry","_id":"9818","intvolume":"        40","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"type":"journal_article","oa_version":"Published Version","volume":40,"article_processing_charge":"Yes (in subscription journal)","date_created":"2021-08-08T22:01:27Z","oa":1,"quality_controlled":"1","article_number":"168","ddc":["000"],"article_type":"original","publisher":"Association for Computing Machinery","abstract":[{"text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.","lang":"eng"}],"status":"public","month":"08","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication":"ACM Transactions on Graphics","ec_funded":1},{"citation":{"mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>, vol. 213, no. 4, 107808, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” <i>Journal of Structural Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. 2021;213(4). doi:<a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">10.1016/j.jsb.2021.107808</a>","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2021.107808\">https://doi.org/10.1016/j.jsb.2021.107808</a>","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” <i>Journal of Structural Biology</i>, vol. 213, no. 4. Elsevier, 2021."},"publication_status":"published","author":[{"orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Falcke, Martin","first_name":"Martin","last_name":"Falcke"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"corr_author":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"grant_number":"M02495","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","_id":"10290","das_tickbox":"1","intvolume":"       213","department":[{"_id":"FlSc"}],"type":"journal_article","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"software","id":"14502"}]},"keyword":["Structural Biology"],"isi":1,"issue":"4","language":[{"iso":"eng"}],"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 Victor-Valentin Hodirnau for help with cryo-ET data acquisition. 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.","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","creator":"cchlebak","date_created":"2021-11-15T13:11:27Z","success":1,"file_id":"10291","relation":"main_file","date_updated":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","file_name":"2021_JournalStructBiol_Dimchev.pdf","content_type":"application/pdf","file_size":16818304}],"external_id":{"isi":["000720259500002"]},"date_published":"2021-11-03T00:00:00Z","date_updated":"2026-07-06T12:57:43Z","doi":"10.1016/j.jsb.2021.107808","year":"2021","day":"03","publication_identifier":{"issn":["1047-8477"]},"publication":"Journal of Structural Biology","article_processing_charge":"Yes (via OA deal)","volume":213,"date_created":"2021-11-15T12:21:42Z","oa":1,"quality_controlled":"1","article_number":"107808","ddc":["572"],"article_type":"original","file_date_updated":"2021-11-15T13:11:27Z","publisher":"Elsevier","abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"status":"public","month":"11"},{"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","language":[{"iso":"eng"}],"issue":"12","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19386"}]},"keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"year":"2021","day":"19","doi":"10.1093/molbev/msab178","date_updated":"2026-07-25T22:31:05Z","date_published":"2021-06-19T00:00:00Z","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-05-06T09:47:18Z","creator":"dernst","access_level":"open_access","file_id":"11352","success":1,"date_updated":"2022-05-06T09:47:18Z","relation":"main_file","file_size":1008594,"content_type":"application/pdf","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf"}],"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","corr_author":"1","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"publication_status":"published","author":[{"first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"},{"first_name":"Mikhail A.","last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A.","orcid":"0000-0002-8876-6494"},{"full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"citation":{"ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press, 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press, pp. 5345–58, 2021.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>"},"oa_version":"Published Version","type":"journal_article","department":[{"_id":"BeVi"}],"intvolume":"       138","das_tickbox":"1","_id":"10167","publisher":"Oxford University Press","file_date_updated":"2022-05-06T09:47:18Z","article_type":"original","ddc":["610"],"quality_controlled":"1","date_created":"2021-10-21T07:49:12Z","oa":1,"volume":138,"article_processing_charge":"No","month":"06","status":"public","abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"page":"5345-58","publication":"Molecular Biology and Evolution","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]}},{"publication":"IEEE Transactions on Visualization and Computer Graphics","publication_identifier":{"issn":["1077-2626"],"eissn":["1941-0506"]},"month":"06","status":"public","abstract":[{"text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.","lang":"eng"}],"page":"2288-2302","publisher":"IEEE","file_date_updated":"2020-10-08T08:34:53Z","article_type":"original","ddc":["006"],"quality_controlled":"1","oa":1,"date_created":"2018-12-16T22:59:21Z","article_processing_charge":"No","volume":26,"oa_version":"Submitted Version","type":"journal_article","intvolume":"        26","department":[{"_id":"ChWo"}],"_id":"5681","title":"Simulating liquids on dynamically warping grids","author":[{"last_name":"Hikaru","first_name":"Ibayashi","full_name":"Hikaru, Ibayashi"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"}],"publication_status":"published","citation":{"ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., &#38; Ando, R. (2020). Simulating liquids on dynamically warping grids. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">https://doi.org/10.1109/TVCG.2018.2883628</a>","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2020;26(6):2288-2302. doi:<a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">10.1109/TVCG.2018.2883628</a>","mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:<a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">10.1109/TVCG.2018.2883628</a>.","ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">https://doi.org/10.1109/TVCG.2018.2883628</a>."},"pmid":1,"day":"01","year":"2020","doi":"10.1109/TVCG.2018.2883628","date_published":"2020-06-01T00:00:00Z","date_updated":"2025-07-10T11:52:55Z","file":[{"file_size":21910098,"file_name":"preprint.pdf","checksum":"8d4c55443a0ee335bb5bb652de503042","content_type":"application/pdf","date_updated":"2020-10-08T08:34:53Z","relation":"main_file","file_id":"8626","success":1,"creator":"wojtan","date_created":"2020-10-08T08:34:53Z","access_level":"open_access"}],"external_id":{"pmid":["30507534"],"isi":["000532295600014"]},"acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.","language":[{"iso":"eng"}],"issue":"6","isi":1,"scopus_import":"1","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"}]},{"article_processing_charge":"No","volume":33,"quality_controlled":"1","oa":1,"date_created":"2020-07-31T16:59:19Z","publisher":"Neural Information Processing Systems Foundation","page":"3106–3117","status":"public","abstract":[{"lang":"eng","text":"A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that\r\ngives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to\r\ngenerate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on\r\ndepth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking."}],"month":"07","publication_identifier":{"isbn":["9781713829546"]},"conference":{"start_date":"2020-12-06","name":"NeurIPS: Neural Information Processing Systems","end_date":"2020-12-12","location":"Vancouver, Canada"},"publication":"34th Conference on Neural Information Processing Systems","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Advances in Neural Information Processing Systems"],"main_file_link":[{"url":"https://arxiv.org/abs/2007.06705","open_access":"1"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). PH is employed part-time by Blackford Analysis, but\r\nthey did not support this project in any way.","language":[{"iso":"eng"}],"external_id":{"arxiv":["2007.06705"]},"date_updated":"2025-05-14T11:26:57Z","date_published":"2020-07-07T00:00:00Z","day":"07","year":"2020","corr_author":"1","citation":{"apa":"Henderson, P. M., &#38; Lampert, C. (2020). Unsupervised object-centric video generation and decomposition in 3D. In <i>34th Conference on Neural Information Processing Systems</i> (Vol. 33, pp. 3106–3117). Vancouver, Canada: Neural Information Processing Systems Foundation.","ieee":"P. M. Henderson and C. Lampert, “Unsupervised object-centric video generation and decomposition in 3D,” in <i>34th Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2020, vol. 33, pp. 3106–3117.","ama":"Henderson PM, Lampert C. Unsupervised object-centric video generation and decomposition in 3D. In: <i>34th Conference on Neural Information Processing Systems</i>. Vol 33. Neural Information Processing Systems Foundation; 2020:3106–3117.","mla":"Henderson, Paul M., and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” <i>34th Conference on Neural Information Processing Systems</i>, vol. 33, Neural Information Processing Systems Foundation, 2020, pp. 3106–3117.","ista":"Henderson PM, Lampert C. 2020. Unsupervised object-centric video generation and decomposition in 3D. 34th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 33, 3106–3117.","short":"P.M. Henderson, C. Lampert, in:, 34th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2020, pp. 3106–3117.","chicago":"Henderson, Paul M, and Christoph Lampert. “Unsupervised Object-Centric Video Generation and Decomposition in 3D.” In <i>34th Conference on Neural Information Processing Systems</i>, 33:3106–3117. Neural Information Processing Systems Foundation, 2020."},"author":[{"full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445","first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"publication_status":"published","title":"Unsupervised object-centric video generation and decomposition in 3D","arxiv":1,"_id":"8188","department":[{"_id":"ChLa"}],"intvolume":"        33","type":"conference","oa_version":"Preprint"},{"title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","author":[{"full_name":"Zhang, Xiaomin","first_name":"Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"publication_status":"published","citation":{"chicago":"Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>.","short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","ista":"Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.","mla":"Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, pp. 1212–25, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>.","ama":"Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. 2020;107(6):1212-1225. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">10.1016/j.neuron.2020.07.006</a>","ieee":"X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information flow from input to output in hippocampal granule cells,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, pp. 1212–1225, 2020.","apa":"Zhang, X., Schlögl, A., &#38; Jonas, P. M. (2020). Selective routing of spatial information flow from input to output in hippocampal granule cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.07.006\">https://doi.org/10.1016/j.neuron.2020.07.006</a>"},"project":[{"grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","intvolume":"       107","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"_id":"8261","oa_version":"Published Version","type":"journal_article","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","relation":"press_release","description":"News on IST Website"}]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari, Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp recording. We are grateful to Florian Marr for cell labeling, cell reconstruction, and technical assistance; Ben Suter for helpful discussions; Christina Altmutter for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor Asenov (Machine Shop) for device construction. We also thank the Scientific Service Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical Facility) for efficient support.","isi":1,"issue":"6","date_published":"2020-09-23T00:00:00Z","date_updated":"2025-04-15T08:29:03Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"file":[{"file_size":3011120,"content_type":"application/pdf","checksum":"44a5960fc083a4cb3488d22224859fdc","file_name":"2020_Neuron_Zhang.pdf","date_updated":"2020-12-04T09:29:21Z","relation":"main_file","file_id":"8920","success":1,"date_created":"2020-12-04T09:29:21Z","creator":"dernst","access_level":"open_access"}],"day":"23","year":"2020","pmid":1,"doi":"10.1016/j.neuron.2020.07.006","publication_identifier":{"issn":["0896-6273"]},"ec_funded":1,"publication":"Neuron","date_created":"2020-08-14T09:36:05Z","oa":1,"quality_controlled":"1","volume":107,"article_processing_charge":"No","article_type":"original","file_date_updated":"2020-12-04T09:29:21Z","publisher":"Elsevier","ddc":["570"],"page":"1212-1225","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"09","abstract":[{"lang":"eng","text":"Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion."}],"status":"public"},{"doi":"10.15479/AT:ISTA:8353","year":"2020","day":"09","file":[{"file_size":117547589,"content_type":"application/pdf","file_name":"Thesis_Julia_Steiner_pdfA.pdf","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","relation":"main_file","file_id":"8354","date_created":"2020-09-09T14:22:35Z","creator":"jsteiner","access_level":"open_access"},{"file_size":223328668,"checksum":"ba112f957b7145462d0ab79044873ee9","file_name":"Thesis_Julia_Steiner.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-09-15T08:48:37Z","relation":"source_file","file_id":"8355","creator":"jsteiner","date_created":"2020-09-09T14:23:25Z","access_level":"closed"}],"date_updated":"2026-04-08T07:23:36Z","date_published":"2020-09-09T00:00:00Z","alternative_title":["ISTA Thesis"],"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.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8284"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","type":"dissertation","oa_version":"None","_id":"8353","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"department":[{"_id":"LeSa"}],"OA_place":"publisher","project":[{"name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741"}],"corr_author":"1","publication_status":"published","author":[{"full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775","last_name":"Steiner","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"}],"citation":{"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>.","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/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.","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>","ieee":"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>"},"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","status":"public","abstract":[{"text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.","lang":"eng"}],"month":"09","page":"191","ddc":["572"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-16T12:40:56Z","article_processing_charge":"No","date_created":"2020-09-09T14:27:01Z","oa":1,"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]}},{"publication_identifier":{"isbn":["978-3-99078-010-7"],"issn":["2663-337X"]},"degree_awarded":"PhD","ec_funded":1,"page":"118","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."}],"status":"public","month":"09","article_processing_charge":"No","date_created":"2020-09-10T16:19:55Z","oa":1,"ddc":["000"],"file_date_updated":"2020-09-16T15:11:01Z","publisher":"Institute of Science and Technology Austria","_id":"8366","department":[{"_id":"BeBi"}],"supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","oa_version":"Published Version","author":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan"}],"citation":{"ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. <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>.","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","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>","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>"},"publication_status":"published","OA_place":"publisher","corr_author":"1","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767"}],"title":"Computational design of curved thin shells: From glass façades to programmable matter","file":[{"access_level":"open_access","creator":"rguseino","date_created":"2020-09-10T16:11:49Z","success":1,"file_id":"8367","relation":"main_file","date_updated":"2020-09-10T16:11:49Z","file_name":"thesis_rguseinov.pdf","checksum":"f8da89553da36037296b0a80f14ebf50","content_type":"application/pdf","file_size":70950442},{"date_updated":"2020-09-16T15:11:01Z","relation":"source_file","file_size":76207597,"content_type":"application/x-zip-compressed","checksum":"e8fd944c960c20e0e27e6548af69121d","file_name":"thesis_source.zip","date_created":"2020-09-11T09:39:48Z","creator":"rguseino","access_level":"closed","file_id":"8374"}],"date_published":"2020-09-21T00:00:00Z","date_updated":"2026-04-08T07:25:22Z","doi":"10.15479/AT:ISTA:8366","day":"21","year":"2020","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8562"},{"relation":"research_data","id":"8375","status":"public"},{"id":"7151","relation":"research_data","status":"deleted"},{"id":"1001","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7262"}]},"keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"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."},{"quality_controlled":"1","date_created":"2020-09-13T22:01:18Z","oa":1,"article_processing_charge":"No","volume":39,"publisher":"Association for Computing Machinery","article_type":"original","file_date_updated":"2020-11-23T09:03:19Z","article_number":"31","ddc":["000"],"month":"07","status":"public","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"ec_funded":1,"publication":"ACM Transactions on Graphics","related_material":{"record":[{"id":"19630","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"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.","language":[{"iso":"eng"}],"issue":"4","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392405"}],"isi":1,"date_published":"2020-07-08T00:00:00Z","date_updated":"2026-04-16T08:29:36Z","external_id":{"isi":["000583700300004"]},"file":[{"success":1,"file_id":"8795","access_level":"open_access","date_created":"2020-11-23T09:03:19Z","creator":"dernst","content_type":"application/pdf","file_name":"2020_soapfilm_submitted.pdf","checksum":"813831ca91319d794d9748c276b24578","file_size":14935529,"relation":"main_file","date_updated":"2020-11-23T09:03:19Z"}],"year":"2020","day":"08","doi":"10.1145/3386569.3392405","title":"A model for soap film dynamics with evolving thickness","project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"publication_status":"published","author":[{"full_name":"Ishida, Sadashige","orcid":"0000-0002-3121-3100","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","first_name":"Sadashige"},{"id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak","first_name":"Peter","full_name":"Synak, Peter"},{"last_name":"Narita","first_name":"Fumiya","full_name":"Narita, Fumiya"},{"full_name":"Hachisuka, Toshiya","last_name":"Hachisuka","first_name":"Toshiya"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"citation":{"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>.","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>.","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","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.","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>","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>","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."},"department":[{"_id":"ChWo"}],"intvolume":"        39","_id":"8384","oa_version":"Submitted Version","type":"journal_article"},{"article_processing_charge":"No","volume":39,"date_created":"2020-09-13T22:01:18Z","oa":1,"quality_controlled":"1","ddc":["000"],"article_number":"48","article_type":"original","file_date_updated":"2020-11-23T09:01:22Z","publisher":"Association for Computing Machinery","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"}],"status":"public","month":"07","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication":"ACM Transactions on Graphics","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12358"}]},"isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392412"}],"issue":"4","language":[{"iso":"eng"}],"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.","file":[{"access_level":"open_access","creator":"dernst","date_created":"2020-11-23T09:01:22Z","success":1,"file_id":"8794","relation":"main_file","date_updated":"2020-11-23T09:01:22Z","checksum":"cf4c1d361c3196c4bd424520a5588205","file_name":"2020_hylc_submitted.pdf","content_type":"application/pdf","file_size":38922662}],"external_id":{"isi":["000583700300021"]},"date_updated":"2026-04-16T08:31:55Z","date_published":"2020-07-08T00:00:00Z","doi":"10.1145/3386569.3392412","year":"2020","day":"08","author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","first_name":"Georg"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"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>.","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>.","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","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>","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>","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."},"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"corr_author":"1","title":"Homogenized yarn-level cloth","_id":"8385","department":[{"_id":"ChWo"}],"intvolume":"        39","type":"journal_article","oa_version":"Submitted Version"},{"file":[{"file_id":"8391","success":1,"creator":"dernst","date_created":"2020-09-14T13:39:14Z","access_level":"open_access","file_size":30224591,"file_name":"2020_Thesis_Royer.pdf","checksum":"c914d2f88846032f3d8507734861b6ee","content_type":"application/pdf","date_updated":"2020-09-14T13:39:14Z","relation":"main_file"},{"file_size":74227627,"file_name":"thesis_sources.zip","checksum":"ae98fb35d912cff84a89035ae5794d3c","content_type":"application/x-zip-compressed","date_updated":"2020-09-14T13:39:17Z","relation":"main_file","file_id":"8392","creator":"dernst","date_created":"2020-09-14T13:39:17Z","access_level":"closed"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","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"},"date_updated":"2026-04-08T07:26:44Z","date_published":"2020-09-14T00:00:00Z","doi":"10.15479/AT:ISTA:8390","year":"2020","day":"14","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"status":"public","id":"7936","relation":"part_of_dissertation"},{"id":"8092","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"911","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8193"},{"id":"7937","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"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.","_id":"8390","department":[{"_id":"ChLa"}],"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"type":"dissertation","oa_version":"Published Version","publication_status":"published","author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","first_name":"Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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>","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","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>","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","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>.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","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>."},"corr_author":"1","OA_place":"publisher","title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","page":"197","abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"status":"public","month":"09","article_processing_charge":"No","oa":1,"date_created":"2020-09-14T13:42:09Z","ddc":["000"],"file_date_updated":"2020-09-14T13:39:17Z","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"degree_awarded":"PhD"},{"status":"public","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"}],"month":"07","article_number":"65","ddc":["000"],"publisher":"Association for Computing Machinery","article_type":"original","file_date_updated":"2020-09-21T07:51:44Z","volume":39,"article_processing_charge":"No","quality_controlled":"1","oa":1,"date_created":"2020-09-20T22:01:37Z","publication":"ACM Transactions on Graphics","ec_funded":1,"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"doi":"10.1145/3386569.3392466","day":"08","year":"2020","file":[{"file_id":"8541","success":1,"date_created":"2020-09-21T07:51:44Z","creator":"dernst","access_level":"open_access","file_size":20223953,"content_type":"application/pdf","checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","file_name":"2020_ACM_Skrivan.pdf","date_updated":"2020-09-21T07:51:44Z","relation":"main_file"}],"external_id":{"isi":["000583700300038"]},"date_updated":"2026-04-16T08:26:38Z","date_published":"2020-07-08T00:00:00Z","issue":"4","isi":1,"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.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","type":"journal_article","oa_version":"Published Version","_id":"8535","department":[{"_id":"ChWo"}],"intvolume":"        39","project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"corr_author":"1","citation":{"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>.","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>.","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","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>","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.","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>"},"author":[{"full_name":"Skrivan, Tomas","first_name":"Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Soderstrom, Andreas","last_name":"Soderstrom","first_name":"Andreas"},{"first_name":"John","last_name":"Johansson","full_name":"Johansson, John"},{"first_name":"Christoph","last_name":"Sprenger","full_name":"Sprenger, Christoph"},{"first_name":"Ken","last_name":"Museth","full_name":"Museth, Ken"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"publication_status":"published","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces"},{"department":[{"_id":"BeBi"}],"intvolume":"        39","_id":"8562","oa_version":"Submitted Version","type":"journal_article","title":"Computational design of cold bent glass façades","corr_author":"1","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767"}],"citation":{"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>","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.","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>","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).","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.","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>."},"author":[{"first_name":"Konstantinos","last_name":"Gavriil","full_name":"Gavriil, Konstantinos"},{"orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan"},{"full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"first_name":"Davide","last_name":"Pellis","full_name":"Pellis, Davide"},{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","first_name":"Paul M","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"full_name":"Rist, Florian","last_name":"Rist","first_name":"Florian"},{"first_name":"Helmut","last_name":"Pottmann","full_name":"Pottmann, Helmut"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"publication_status":"published","arxiv":1,"date_published":"2020-11-26T00:00:00Z","date_updated":"2026-04-08T07:25:22Z","file":[{"date_updated":"2023-05-23T20:54:43Z","relation":"main_file","file_size":28964641,"checksum":"c7f67717ad74e670b7daeae732abe151","file_name":"coldglass.pdf","content_type":"application/pdf","creator":"bbickel","date_created":"2023-05-23T20:54:43Z","access_level":"open_access","file_id":"13084","success":1}],"external_id":{"isi":["000595589100048"],"arxiv":["2009.03667"]},"year":"2020","day":"26","doi":"10.1145/3414685.3417843","related_material":{"record":[{"status":"public","id":"8761","relation":"research_data"},{"id":"8366","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/bend-dont-break/"}]},"scopus_import":"1","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"ScienComp"}],"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.","language":[{"iso":"eng"}],"issue":"6","isi":1,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"ec_funded":1,"publication":"ACM Transactions on Graphics","month":"11","status":"public","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","oa":1,"date_created":"2020-09-23T11:30:02Z","volume":39,"article_processing_charge":"No","publisher":"Association for Computing Machinery","file_date_updated":"2023-05-23T20:54:43Z","article_type":"original","ddc":["000"],"article_number":"208"},{"date_published":"2020-11-01T00:00:00Z","date_updated":"2025-07-10T11:57:09Z","external_id":{"pmid":["32929284"],"isi":["000569299400004"]},"day":"01","year":"2020","pmid":1,"doi":"10.1038/s41594-020-0503-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/"}]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"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.","isi":1,"issue":"11","department":[{"_id":"LeSa"}],"intvolume":"        27","_id":"8581","oa_version":"None","type":"journal_article","title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","author":[{"first_name":"Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","last_name":"Pinke","full_name":"Pinke, Gergely"},{"id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou","first_name":"Long","orcid":"0000-0002-1864-8951","full_name":"Zhou, Long"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"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>","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>","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.","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>.","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>."},"publication_status":"published","page":"1077-1085","month":"11","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"}],"status":"public","date_created":"2020-09-28T08:59:27Z","quality_controlled":"1","article_processing_charge":"No","volume":27,"article_type":"original","publisher":"Springer Nature","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"publication":"Nature Structural and Molecular Biology"},{"publication_identifier":{"issn":["2640-3498"]},"conference":{"start_date":"2020-07-12","name":"ICML: International Conference on Machine Learning","location":"Online","end_date":"2020-07-18"},"publication":"Proceedings of the 37th International Conference on Machine Learning","ec_funded":1,"page":"5416-5425","status":"public","abstract":[{"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. ","lang":"eng"}],"month":"07","article_processing_charge":"No","volume":119,"quality_controlled":"1","date_created":"2020-11-05T15:25:58Z","oa":1,"ddc":["000"],"publisher":"ML Research Press","file_date_updated":"2021-02-15T09:00:01Z","_id":"8724","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"intvolume":"       119","type":"conference","oa_version":"Published Version","corr_author":"1","project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"publication_status":"published","citation":{"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.","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.","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.","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.","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.","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.","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."},"author":[{"first_name":"Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0009-5204-7621","full_name":"Konstantinov, Nikola H"},{"first_name":"Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"title":"On the sample complexity of adversarial multi-source PAC learning","arxiv":1,"external_id":{"arxiv":["2002.10384"]},"file":[{"success":1,"file_id":"9120","access_level":"open_access","date_created":"2021-02-15T09:00:01Z","creator":"dernst","content_type":"application/pdf","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","file_name":"2020_PMLR_Konstantinov.pdf","file_size":281286,"relation":"main_file","date_updated":"2021-02-15T09:00:01Z"}],"date_published":"2020-07-12T00:00:00Z","date_updated":"2026-04-07T14:19:48Z","year":"2020","day":"12","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"id":"10799","relation":"dissertation_contains","status":"public"}],"link":[{"url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf","relation":"supplementary_material"}]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"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).","language":[{"iso":"eng"}]},{"_id":"8761","department":[{"_id":"BeBi"}],"type":"research_data","oa_version":"Published Version","ec_funded":1,"corr_author":"1","project":[{"grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"citation":{"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>","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>","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020.","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>.","short":"R. Guseinov, (2020).","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>.","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>."},"author":[{"first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077"}],"title":"Supplementary data for \"Computational design of cold bent glass façades\"","contributor":[{"last_name":"Gavriil","first_name":"Konstantinos","contributor_type":"researcher"},{"last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez"},{"contributor_type":"researcher","last_name":"Pellis","first_name":"Davide"},{"orcid":"0000-0002-5198-7445","contributor_type":"researcher","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","first_name":"Paul M"},{"contributor_type":"researcher","first_name":"Florian","last_name":"Rist"},{"contributor_type":"researcher","last_name":"Pottmann","first_name":"Helmut"},{"orcid":"0000-0001-6511-9385","contributor_type":"researcher","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"file":[{"file_id":"8762","success":1,"creator":"rguseino","date_created":"2020-11-16T10:31:29Z","access_level":"open_access","file_size":15378270,"checksum":"f5ae57b97017b9f61081032703361233","file_name":"mdn_model.tar.gz","content_type":"application/x-gzip","date_updated":"2020-11-16T10:31:29Z","relation":"main_file"},{"file_id":"8763","success":1,"date_created":"2020-11-16T10:43:23Z","creator":"rguseino","access_level":"open_access","file_size":615387734,"content_type":"application/x-gzip","file_name":"optimal_panels_data.tar.gz","checksum":"b0d25e04060ee78c585ee2f23542c744","date_updated":"2020-11-16T10:43:23Z","relation":"main_file"},{"creator":"rguseino","date_created":"2020-11-18T10:04:59Z","access_level":"open_access","file_id":"8770","success":1,"date_updated":"2020-11-18T10:04:59Z","relation":"main_file","file_size":1228,"checksum":"69c1dde3434ada86d125e0c2588caf1e","file_name":"readme.txt","content_type":"text/plain"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2020-11-23T00:00:00Z","date_updated":"2025-04-15T07:16:12Z","status":"public","doi":"10.15479/AT:ISTA:8761","month":"11","day":"23","year":"2020","article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"relation":"used_in_publication","id":"8562","status":"public"}],"link":[{"url":"https://github.com/russelmann/cold-glass-acm","relation":"software"}]},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_created":"2020-11-16T10:47:18Z","ddc":["000"],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-11-18T10:04:59Z"},{"publication":"Computer Graphics Forum","ec_funded":1,"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"ddc":["000"],"article_type":"original","file_date_updated":"2020-11-23T09:05:13Z","publisher":"Wiley","article_processing_charge":"No","volume":39,"oa":1,"date_created":"2020-11-17T09:35:10Z","quality_controlled":"1","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"}],"status":"public","month":"05","page":"89-99","citation":{"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>.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 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>.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","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>","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>","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."},"author":[{"full_name":"Schreck, Camille","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"title":"A practical method for animating anisotropic elastoplastic materials","type":"journal_article","oa_version":"Submitted Version","_id":"8765","department":[{"_id":"ChWo"}],"intvolume":"        39","isi":1,"issue":"2","language":[{"iso":"eng"}],"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.","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","scopus_import":"1","keyword":["Computer Networks and Communications"],"doi":"10.1111/cgf.13914","year":"2020","day":"01","file":[{"access_level":"open_access","creator":"dernst","date_created":"2020-11-23T09:05:13Z","success":1,"file_id":"8796","relation":"main_file","date_updated":"2020-11-23T09:05:13Z","file_name":"2020_poff_revisited.pdf","checksum":"7605f605acd84d0942b48bc7a1c2d72e","content_type":"application/pdf","file_size":38969122}],"external_id":{"isi":["000548709600008"]},"date_updated":"2024-10-22T09:58:14Z","date_published":"2020-05-01T00:00:00Z"},{"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","relation":"press_release","description":"News on IST Homepage"}]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"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. ","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","date_created":"2020-12-28T08:16:10Z","creator":"dernst","success":1,"file_id":"8975","relation":"main_file","date_updated":"2020-12-28T08:16:10Z","content_type":"application/pdf","checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_name":"2020_NatureComm_Faessler.pdf","file_size":3958727}],"external_id":{"isi":["000603078000003"]},"date_published":"2020-12-22T00:00:00Z","date_updated":"2025-04-15T07:52:12Z","doi":"10.1038/s41467-020-20286-x","year":"2020","day":"22","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","grant_number":"M02495"}],"corr_author":"1","publication_status":"published","citation":{"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>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (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>.","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.","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>","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>","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."},"author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","orcid":"0000-0001-8370-6161","full_name":"Dimchev, Georgi A"},{"first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"William","last_name":"Wan","full_name":"Wan, William"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","_id":"8971","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"intvolume":"        11","type":"journal_article","oa_version":"Published Version","volume":11,"article_processing_charge":"No","quality_controlled":"1","oa":1,"date_created":"2020-12-23T08:25:45Z","article_number":"6437","ddc":["570"],"publisher":"Springer Nature","file_date_updated":"2020-12-28T08:16:10Z","article_type":"original","status":"public","abstract":[{"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.","lang":"eng"}],"month":"12","publication_identifier":{"issn":["2041-1723"]},"publication":"Nature Communications"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","related_material":{"record":[{"status":"deleted","relation":"research_data","id":"9723"}]},"scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"isi":1,"issue":"1","date_published":"2020-01-27T00:00:00Z","date_updated":"2025-04-15T08:24:51Z","external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":4551246,"checksum":"a297f54d1fef0efe4789ca00f37f241e","file_name":"2020_PLOSPatho_Dick.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:59Z","relation":"main_file","file_id":"7484","creator":"dernst","date_created":"2020-02-11T10:07:28Z","access_level":"open_access"}],"year":"2020","day":"27","pmid":1,"doi":"10.1371/journal.ppat.1008277","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","citation":{"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.","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>","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>","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>.","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>.","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_status":"published","author":[{"full_name":"Dick, Robert A.","last_name":"Dick","first_name":"Robert A."},{"full_name":"Xu, Chaoyi","last_name":"Xu","first_name":"Chaoyi"},{"last_name":"Morado","first_name":"Dustin R.","full_name":"Morado, Dustin R."},{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","first_name":"Vladyslav","orcid":"0000-0001-9523-9089","full_name":"Kravchuk, Vladyslav"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Lyddon, Terri D.","last_name":"Lyddon","first_name":"Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"last_name":"Feathers","first_name":"J. Ryan","full_name":"Feathers, J. Ryan"},{"last_name":"Johnson","first_name":"Marc C.","full_name":"Johnson, Marc C."},{"full_name":"Vogt, Volker M.","first_name":"Volker M.","last_name":"Vogt"},{"last_name":"Perilla","first_name":"Juan R.","full_name":"Perilla, Juan R."},{"last_name":"Briggs","first_name":"John A. G.","full_name":"Briggs, John A. G."},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"corr_author":"1","project":[{"grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"intvolume":"        16","department":[{"_id":"FlSc"}],"_id":"7464","oa_version":"Published Version","type":"journal_article","oa":1,"date_created":"2020-02-06T18:47:17Z","quality_controlled":"1","volume":16,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","article_type":"original","publisher":"Public Library of Science","ddc":["570"],"article_number":"e1008277","month":"01","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"}],"status":"public","publication_identifier":{"issn":["1553-7374"]},"publication":"PLOS Pathogens"},{"issue":"3","isi":1,"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.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"scopus_import":"1","related_material":{"record":[{"id":"14592","relation":"used_in_publication","status":"public"},{"id":"12491","relation":"dissertation_contains","status":"public"}]},"keyword":["electron microscopy","cryo-EM","EM sample preparation","3D printing","cell culture"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","doi":"10.1016/j.jsb.2020.107633","pmid":1,"day":"01","year":"2020","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["32987119"],"isi":["000600997800008"]},"file":[{"file_size":7076870,"content_type":"application/pdf","file_name":"2020_JourStrucBiology_Faessler.pdf","checksum":"c48cbf594e84fc2f91966ffaafc0918c","date_updated":"2020-12-10T14:01:10Z","relation":"main_file","file_id":"8937","success":1,"date_created":"2020-12-10T14:01:10Z","creator":"dernst","access_level":"open_access"}],"date_published":"2020-12-01T00:00:00Z","date_updated":"2026-07-25T22:30:03Z","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"corr_author":"1","publication_status":"published","author":[{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"citation":{"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>.","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.","short":"F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology 212 (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>.","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.","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>","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>"},"title":"3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","type":"journal_article","oa_version":"Published Version","_id":"8586","intvolume":"       212","department":[{"_id":"FlSc"}],"ddc":["570"],"article_number":"107633","publisher":"Elsevier","file_date_updated":"2020-12-10T14:01:10Z","article_type":"original","article_processing_charge":"Yes (via OA deal)","volume":212,"quality_controlled":"1","oa":1,"date_created":"2020-09-29T13:24:06Z","status":"public","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."}],"month":"12","publication":"Journal of Structural Biology","publication_identifier":{"issn":["1047-8477"]}}]