[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ec_funded":1,"publication_status":"published","issue":"6","fulldoi":"https://doi.org/10.1016/j.neuron.2020.07.006","date_updated":"2025-04-15T08:29:03Z","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","pmid":1,"status":"public","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"}],"doi":"10.1016/j.neuron.2020.07.006","isi":1,"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"date_published":"2020-09-23T00:00:00Z","ddc":["570"],"citation":{"short":"X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.","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.","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>.","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.","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>","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>","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>."},"oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["32763145"],"isi":["000579698700009"]},"month":"09","related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/the-bouncer-in-the-brain/","relation":"press_release"}]},"abstract":[{"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.","lang":"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.","day":"23","volume":107,"publication":"Neuron","oa":1,"intvolume":"       107","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"year":"2020","corr_author":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-12-04T09:29:21Z","date_created":"2020-08-14T09:36:05Z","_id":"8261","page":"1212-1225","title":"Selective routing of spatial information flow from input to output in hippocampal granule cells","quality_controlled":"1","author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"article_type":"original","publication_identifier":{"issn":["0896-6273"]},"publisher":"Elsevier","file":[{"content_type":"application/pdf","date_created":"2020-12-04T09:29:21Z","file_name":"2020_Neuron_Zhang.pdf","date_updated":"2020-12-04T09:29:21Z","file_size":3011120,"file_id":"8920","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"checksum":"44a5960fc083a4cb3488d22224859fdc"}],"scopus_import":"1"},{"acknowledgement":"The authors would like to thank Dr. Michiel Brentjens at the Netherlands Institute for Radio Astronomy (ASTRON) for providing radio interferometer data and Dr. Josip Marjanovic and Dr. Franciszek Hennel at the Magnetic Resonance Technology of ETH Zurich for providing their insights on the experiments. CZ and the DS3Lab gratefully acknowledge the support from the Swiss Data Science Center, Alibaba, Google Focused Research Awards, Huawei, MeteoSwiss, Oracle Labs, Swisscom, Zurich Insurance, Chinese Scholarship Council, and the Department of Computer Science at ETH Zurich.","arxiv":1,"day":"20","publication":"IEEE Transactions on Signal Processing","volume":68,"oa":1,"intvolume":"        68","year":"2020","language":[{"iso":"eng"}],"_id":"8268","page":"4268-4282","date_created":"2020-08-16T22:00:56Z","title":"Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications","quality_controlled":"1","author":[{"last_name":"Gurel","full_name":"Gurel, Nezihe Merve","first_name":"Nezihe Merve"},{"full_name":"Kara, Kaan","last_name":"Kara","first_name":"Kaan"},{"first_name":"Alen","last_name":"Stojanov","full_name":"Stojanov, Alen"},{"first_name":"Tyler","last_name":"Smith","full_name":"Smith, Tyler"},{"full_name":"Lemmin, Thomas","last_name":"Lemmin","first_name":"Thomas"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Puschel, Markus","last_name":"Puschel","first_name":"Markus"},{"first_name":"Ce","full_name":"Zhang, Ce","last_name":"Zhang"}],"article_type":"original","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"publisher":"IEEE","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","fulldoi":"https://doi.org/10.1109/TSP.2020.3010355","date_updated":"2025-07-10T11:55:10Z","article_processing_charge":"No","department":[{"_id":"DaAl"}],"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1802.04907","open_access":"1"}],"isi":1,"doi":"10.1109/TSP.2020.3010355","date_published":"2020-07-20T00:00:00Z","citation":{"chicago":"Gurel, Nezihe Merve, Kaan Kara, Alen Stojanov, Tyler Smith, Thomas Lemmin, Dan-Adrian Alistarh, Markus Puschel, and Ce Zhang. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>.","ama":"Gurel NM, Kara K, Stojanov A, et al. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. 2020;68:4268-4282. doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>","ista":"Gurel NM, Kara K, Stojanov A, Smith T, Lemmin T, Alistarh D-A, Puschel M, Zhang C. 2020. Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. IEEE Transactions on Signal Processing. 68, 4268–4282.","short":"N.M. Gurel, K. Kara, A. Stojanov, T. Smith, T. Lemmin, D.-A. Alistarh, M. Puschel, C. Zhang, IEEE Transactions on Signal Processing 68 (2020) 4268–4282.","ieee":"N. M. Gurel <i>et al.</i>, “Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications,” <i>IEEE Transactions on Signal Processing</i>, vol. 68. IEEE, pp. 4268–4282, 2020.","mla":"Gurel, Nezihe Merve, et al. “Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications.” <i>IEEE Transactions on Signal Processing</i>, vol. 68, IEEE, 2020, pp. 4268–82, doi:<a href=\"https://doi.org/10.1109/TSP.2020.3010355\">10.1109/TSP.2020.3010355</a>.","apa":"Gurel, N. M., Kara, K., Stojanov, A., Smith, T., Lemmin, T., Alistarh, D.-A., … Zhang, C. (2020). Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications. <i>IEEE Transactions on Signal Processing</i>. IEEE. <a href=\"https://doi.org/10.1109/TSP.2020.3010355\">https://doi.org/10.1109/TSP.2020.3010355</a>"},"oa_version":"Preprint","external_id":{"arxiv":["1802.04907"],"isi":["000562044500001"]},"type":"journal_article","month":"07","abstract":[{"text":"Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.","lang":"eng"}]},{"year":"2020","language":[{"iso":"eng"}],"OA_place":"publisher","oa":1,"intvolume":"        13","volume":13,"publication":"Molecular Plant","day":"07","acknowledgement":"We thank Dr. Gai Huang for his comments and help. We apologize to authors whose work could not be cited due to space limitation. No conflict of interest declared.","publisher":"Elsevier","publication_identifier":{"eissn":["1752-9867"],"issn":["1674-2052"]},"scopus_import":"1","quality_controlled":"1","title":"Origin of a subgenome and genome evolution of allotetraploid cotton species","article_type":"original","author":[{"last_name":"He","full_name":"He, Peng","first_name":"Peng"},{"orcid":"0000-0003-2627-6956","first_name":"Yuzhou","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang"},{"full_name":"Xiao, Guanghui","last_name":"Xiao","first_name":"Guanghui"}],"_id":"8271","page":"1238-1240","date_created":"2020-08-16T22:00:57Z","pmid":1,"article_processing_charge":"No","department":[{"_id":"JiFr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T19:32:01Z","fulldoi":"https://doi.org/10.1016/j.molp.2020.07.006","publication_status":"published","issue":"9","month":"09","oa_version":"Published Version","type":"journal_article","external_id":{"isi":["000566895400007"],"pmid":["32688032"]},"date_published":"2020-09-07T00:00:00Z","citation":{"ieee":"P. He, Y. Zhang, and G. Xiao, “Origin of a subgenome and genome evolution of allotetraploid cotton species,” <i>Molecular Plant</i>, vol. 13, no. 9. Elsevier, pp. 1238–1240, 2020.","short":"P. He, Y. Zhang, G. Xiao, Molecular Plant 13 (2020) 1238–1240.","chicago":"He, Peng, Yuzhou Zhang, and Guanghui Xiao. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>.","ama":"He P, Zhang Y, Xiao G. Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. 2020;13(9):1238-1240. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>","ista":"He P, Zhang Y, Xiao G. 2020. Origin of a subgenome and genome evolution of allotetraploid cotton species. Molecular Plant. 13(9), 1238–1240.","apa":"He, P., Zhang, Y., &#38; Xiao, G. (2020). Origin of a subgenome and genome evolution of allotetraploid cotton species. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">https://doi.org/10.1016/j.molp.2020.07.006</a>","mla":"He, Peng, et al. “Origin of a Subgenome and Genome Evolution of Allotetraploid Cotton Species.” <i>Molecular Plant</i>, vol. 13, no. 9, Elsevier, 2020, pp. 1238–40, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.07.006\">10.1016/j.molp.2020.07.006</a>."},"ddc":["580"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molp.2020.07.006"}],"status":"public","doi":"10.1016/j.molp.2020.07.006","isi":1,"OA_type":"free access"},{"date_created":"2020-08-24T06:24:04Z","_id":"8284","file_date_updated":"2020-08-24T13:31:53Z","scopus_import":"1","file":[{"content_type":"application/pdf","date_updated":"2020-08-24T13:31:53Z","date_created":"2020-08-24T13:31:53Z","file_name":"2020_eLife_Steiner.pdf","file_size":7320493,"success":1,"checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","file_id":"8289","access_level":"open_access","creator":"cziletti","relation":"main_file"}],"publisher":"eLife Sciences Publications","publication_identifier":{"eissn":["2050-084X"]},"author":[{"last_name":"Steiner","full_name":"Steiner, Julia","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","orcid":"0000-0003-0493-3775"},{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"article_type":"original","quality_controlled":"1","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","volume":9,"publication":"eLife","day":"31","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","language":[{"iso":"eng"}],"year":"2020","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"intvolume":"         9","oa":1,"ddc":["570"],"citation":{"apa":"Steiner, J., &#38; Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>, vol. 9, e59407, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>.","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.59407\">https://doi.org/10.7554/eLife.59407</a>.","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.59407\">10.7554/eLife.59407</a>","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"date_published":"2020-07-31T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"doi":"10.7554/eLife.59407","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"status":"public","abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8353","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/"}]},"month":"07","external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"type":"journal_article","oa_version":"Published Version","fulldoi":"https://doi.org/10.7554/eLife.59407","date_updated":"2026-04-08T07:23:36Z","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"e59407","license":"https://creativecommons.org/licenses/by/4.0/","pmid":1,"department":[{"_id":"LeSa"}],"has_accepted_license":"1","article_processing_charge":"No"},{"conference":{"end_date":"2020-09-25","start_date":"2020-09-20","name":"EMSOFT: Embedded Software","location":"Virtual "},"oa":1,"year":"2020","language":[{"iso":"eng"}],"day":"01","arxiv":1,"publication":"Proceedings of the International Conference on Embedded Software","title":"Reachability analysis of linear hybrid systems via block decomposition","quality_controlled":"1","author":[{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"last_name":"Potomkin","full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn"},{"full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","orcid":"0000-0003-3658-1065"}],"file":[{"file_id":"8288","access_level":"open_access","creator":"cschilli","relation":"main_file","success":1,"checksum":"d19e97d0f8a3a441dc078ec812297d75","content_type":"application/pdf","date_updated":"2020-08-24T12:53:15Z","date_created":"2020-08-24T12:53:15Z","file_name":"2020EMSOFT.pdf","file_size":696384}],"file_date_updated":"2020-08-24T12:53:15Z","_id":"8287","date_created":"2020-08-24T12:56:20Z","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"ToHe"}],"keyword":["reachability","hybrid systems","decomposition"],"ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","date_updated":"2026-04-03T09:32:00Z","oa_version":"Preprint","type":"conference","external_id":{"arxiv":["1905.02458"],"isi":["000587712700072"]},"month":"10","related_material":{"record":[{"status":"public","id":"8790","relation":"later_version"}]},"abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","isi":1,"date_published":"2020-10-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["000"],"citation":{"mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>Proceedings of the International Conference on Embedded Software</i>, 2020.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In <i>Proceedings of the International Conference on Embedded Software</i>. Virtual .","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: Embedded Software.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: <i>Proceedings of the International Conference on Embedded Software</i>. ; 2020.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In <i>Proceedings of the International Conference on Embedded Software</i>, 2020.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in <i>Proceedings of the International Conference on Embedded Software</i>, Virtual , 2020.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020."}},{"department":[{"_id":"Bio"}],"oa":1,"has_accepted_license":"1","corr_author":"1","year":"2020","license":"https://opensource.org/licenses/BSD-3-Clause","day":"10","date_updated":"2024-10-09T21:05:14Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:8294","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert"}],"type":"software","title":"RGtracker","abstract":[{"text":"Automated root growth analysis and tracking of root tips. ","lang":"eng"}],"file":[{"file_size":882,"content_type":"text/plain","file_name":"readme.txt","date_updated":"2020-09-08T14:26:31Z","date_created":"2020-09-08T14:26:31Z","creator":"rhauschild","relation":"main_file","file_id":"8346","access_level":"open_access","success":1,"checksum":"108352149987ac6f066e4925bd56e35e"},{"content_type":"application/octet-stream","date_updated":"2020-09-08T14:26:33Z","file_name":"RGtracker.mlappinstall","date_created":"2020-09-08T14:26:33Z","file_size":246121,"file_id":"8347","access_level":"open_access","creator":"rhauschild","relation":"main_file","success":1,"checksum":"ffd6c643b28e0cc7c6d0060a18a7e8ea"}],"month":"09","publisher":"IST Austria","doi":"10.15479/AT:ISTA:8294","status":"public","_id":"8294","date_created":"2020-08-25T12:52:48Z","ddc":["570"],"citation":{"mla":"Hauschild, Robert. <i>RGtracker</i>. IST Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>.","apa":"Hauschild, R. (2020). RGtracker. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">https://doi.org/10.15479/AT:ISTA:8294</a>","ama":"Hauschild R. RGtracker. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>","ista":"Hauschild R. 2020. RGtracker, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">10.15479/AT:ISTA:8294</a>.","chicago":"Hauschild, Robert. “RGtracker.” IST Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8294\">https://doi.org/10.15479/AT:ISTA:8294</a>.","ieee":"R. Hauschild, “RGtracker.” IST Austria, 2020.","short":"R. Hauschild, (2020)."},"file_date_updated":"2020-09-08T14:26:33Z","date_published":"2020-09-10T00:00:00Z","tmp":{"short":"3-Clause BSD","legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","name":"The 3-Clause BSD License"}},{"file_date_updated":"2020-08-26T19:29:00Z","date_created":"2020-08-26T19:27:42Z","_id":"8308","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publisher":"American Physical Society","file":[{"date_created":"2020-08-26T19:28:55Z","date_updated":"2020-08-26T19:28:55Z","file_name":"PhysRevB.102.060202.pdf","content_type":"application/pdf","file_size":488825,"checksum":"716442fa7861323fcc80b93718ca009c","success":1,"access_level":"open_access","file_id":"8309","relation":"main_file","creator":"mserbyn"},{"checksum":"be0abdc8f60fe065ea6dc92e08487122","success":1,"access_level":"open_access","file_id":"8310","creator":"mserbyn","relation":"main_file","date_updated":"2020-08-26T19:29:00Z","file_name":"Supplementary-mbme.pdf","date_created":"2020-08-26T19:29:00Z","content_type":"application/pdf","file_size":711405}],"scopus_import":"1","title":"Stability of mobility edges in disordered interacting systems","quality_controlled":"1","author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","first_name":"Pietro"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"article_type":"original","volume":102,"publication":"Physical Review B","acknowledgement":"Acknowledgments. We acknowledge useful discussions with W. De Roeck and A. Michailidis. P.B. was supported by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385. D.A. was supported by the Swiss National Science Foundation. M.S. was supported by European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). This work benefited from visits to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958 and from the program “Thermalization, Many Body Localization and Hydrodynamics” at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).","arxiv":1,"day":"26","year":"2020","OA_place":"repository","corr_author":"1","language":[{"iso":"eng"}],"oa":1,"intvolume":"       102","date_published":"2020-08-26T00:00:00Z","ddc":["530"],"citation":{"short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).","ieee":"P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” <i>Physical Review B</i>, vol. 102, no. 6. American Physical Society, 2020.","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R).","ama":"Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. 2020;102(6). doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>","chicago":"Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>.","apa":"Brighi, P., Abanin, D. A., &#38; Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>","mla":"Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>."},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"status":"public","doi":"10.1103/physrevb.102.060202","OA_type":"green","isi":1,"month":"08","related_material":{"record":[{"id":"12732","status":"public","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model."}],"oa_version":"Preprint","type":"journal_article","external_id":{"isi":["000562628300001"],"arxiv":["2005.02999"]},"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","issue":"6","fulldoi":"https://doi.org/10.1103/physrevb.102.060202","date_updated":"2026-04-07T13:26:31Z","article_number":"060202(R)","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"MaSe"}]},{"issue":"1","publication_status":"published","date_updated":"2026-04-02T14:36:31Z","fulldoi":"https://doi.org/10.1038/s41467-020-17957-0","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"LeSa"}],"article_processing_charge":"No","has_accepted_license":"1","article_number":"4135","pmid":1,"doi":"10.1038/s41467-020-17957-0","isi":1,"status":"public","citation":{"apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., &#38; Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>.","ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>.","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. 2020;11(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","ieee":"J. Gutierrez-Fernandez <i>et al.</i>, “Key role of quinone in the mechanism of respiratory complex I,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, 2020."},"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2020-08-18T00:00:00Z","type":"journal_article","external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I."}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","relation":"press_release"}]},"month":"08","acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","day":"18","volume":11,"publication":"Nature Communications","intvolume":"        11","oa":1,"language":[{"iso":"eng"}],"year":"2020","file_date_updated":"2020-08-31T13:40:00Z","date_created":"2020-08-30T22:01:10Z","_id":"8318","article_type":"original","author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","last_name":"Gutierrez-Fernandez","full_name":"Gutierrez-Fernandez, Javier","first_name":"Javier"},{"id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","full_name":"Kaszuba, Karol","last_name":"Kaszuba","first_name":"Karol"},{"first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S.","last_name":"Minhas"},{"last_name":"Baradaran","full_name":"Baradaran, Rozbeh","first_name":"Rozbeh"},{"last_name":"Tambalo","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","full_name":"Tambalo, Margherita","first_name":"Margherita"},{"full_name":"Gallagher, David T.","last_name":"Gallagher","first_name":"David T."},{"orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"title":"Key role of quinone in the mechanism of respiratory complex I","quality_controlled":"1","file":[{"checksum":"52b96f41d7d0db9728064c08da00d030","success":1,"relation":"main_file","creator":"cziletti","access_level":"open_access","file_id":"8326","file_size":7527373,"file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","date_created":"2020-08-31T13:40:00Z","date_updated":"2020-08-31T13:40:00Z","content_type":"application/pdf"}],"scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"publisher":"Springer Nature"},{"acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","day":"19","volume":54,"publication":"Molecular Biology","intvolume":"        54","year":"2020","language":[{"iso":"eng"}],"_id":"8320","date_created":"2020-08-30T22:01:11Z","page":"475-484","title":"Expanding the genetic code: Unnatural base pairs in biological systems","quality_controlled":"1","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr"},{"first_name":"P. M.","full_name":"Kolosov, P. M.","last_name":"Kolosov"},{"last_name":"Shuvalova","full_name":"Shuvalova, E. Y.","first_name":"E. Y."},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"article_type":"original","publication_identifier":{"issn":["0026-8933"],"eissn":["1608-3245"]},"publisher":"Springer Nature","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","publication_status":"published","fulldoi":"https://doi.org/10.1134/S0026893320040111","date_updated":"2025-07-10T11:57:02Z","article_processing_charge":"No","department":[{"_id":"FyKo"}],"status":"public","doi":"10.1134/S0026893320040111","isi":1,"date_published":"2020-08-19T00:00:00Z","citation":{"mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molecular Biology</i>, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. 2020;54(4):475-484. doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>."},"oa_version":"None","external_id":{"isi":["000562110300001"]},"type":"journal_article","month":"08","related_material":{"record":[{"status":"public","id":"8321","relation":"original"}]},"abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}]},{"article_processing_charge":"No","department":[{"_id":"FyKo"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:57:03Z","fulldoi":"https://doi.org/10.31857/S0026898420040126","publication_status":"published","issue":"4","oa_version":"None","external_id":{"pmid":["32799218"]},"type":"journal_article","month":"07","related_material":{"record":[{"status":"public","id":"8320","relation":"translation"}]},"abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"status":"public","doi":"10.31857/S0026898420040126","date_published":"2020-07-01T00:00:00Z","citation":{"apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. 2020;54(4):531-541. doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>."},"intvolume":"        54","year":"2020","language":[{"iso":"rus"}],"day":"01","publication":"Molekuliarnaia biologiia","volume":54,"quality_controlled":"1","title":"Expanding the genetic code: Unnatural base pairs in biological systems","article_type":"original","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr","first_name":"Petr"},{"last_name":"Kolosov","full_name":"Kolosov, P. M.","first_name":"P. M."},{"last_name":"Shuvalova","full_name":"Shuvalova, E. Y.","first_name":"E. Y."},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z.","first_name":"E. Z."}],"publisher":"Russian Academy of Sciences","publication_identifier":{"issn":["0026-8984"]},"scopus_import":"1","date_created":"2020-08-30T22:01:11Z","_id":"8321","page":"531-541"},{"publisher":"Springer Nature","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"scopus_import":"1","title":"A farewell to Ricky Pollack","article_type":"letter_note","author":[{"first_name":"János","full_name":"Pach, János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"}],"_id":"8323","date_created":"2020-08-30T22:01:12Z","page":"571-574","year":"2020","language":[{"iso":"eng"}],"corr_author":"1","oa":1,"intvolume":"        64","volume":64,"publication":"Discrete and Computational Geometry","day":"01","month":"10","oa_version":"None","external_id":{"isi":["000561483500001"]},"type":"journal_article","date_published":"2020-10-01T00:00:00Z","citation":{"ieee":"J. Pach, “A farewell to Ricky Pollack,” <i>Discrete and Computational Geometry</i>, vol. 64. Springer Nature, pp. 571–574, 2020.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","ama":"Pach J. A farewell to Ricky Pollack. <i>Discrete and Computational Geometry</i>. 2020;64:571-574. doi:<a href=\"https://doi.org/10.1007/s00454-020-00237-5\">10.1007/s00454-020-00237-5</a>","chicago":"Pach, János. “A Farewell to Ricky Pollack.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00454-020-00237-5\">https://doi.org/10.1007/s00454-020-00237-5</a>.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00237-5\">https://doi.org/10.1007/s00454-020-00237-5</a>","mla":"Pach, János. “A Farewell to Ricky Pollack.” <i>Discrete and Computational Geometry</i>, vol. 64, Springer Nature, 2020, pp. 571–74, doi:<a href=\"https://doi.org/10.1007/s00454-020-00237-5\">10.1007/s00454-020-00237-5</a>."},"main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"status":"public","isi":1,"doi":"10.1007/s00454-020-00237-5","article_processing_charge":"No","department":[{"_id":"HeEd"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-10-09T20:59:55Z","fulldoi":"https://doi.org/10.1007/s00454-020-00237-5","publication_status":"published"},{"article_number":"25","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"POPL","publication_status":"published","fulldoi":"https://doi.org/10.1145/3371093","date_updated":"2025-04-15T06:30:10Z","month":"01","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"oa_version":"Published Version","type":"conference","external_id":{"arxiv":["1902.04744"]},"date_published":"2020-01-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., &#38; Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In <i>Proceedings of the ACM on Programming Languages</i> (Vol. 4). ACM. <a href=\"https://doi.org/10.1145/3371093\">https://doi.org/10.1145/3371093</a>","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 4, no. POPL, 25, ACM, 2020, doi:<a href=\"https://doi.org/10.1145/3371093\">10.1145/3371093</a>.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in <i>Proceedings of the ACM on Programming Languages</i>, 2020, vol. 4, no. POPL.","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In <i>Proceedings of the ACM on Programming Languages</i>, Vol. 4. ACM, 2020. <a href=\"https://doi.org/10.1145/3371093\">https://doi.org/10.1145/3371093</a>.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: <i>Proceedings of the ACM on Programming Languages</i>. Vol 4. ACM; 2020. doi:<a href=\"https://doi.org/10.1145/3371093\">10.1145/3371093</a>","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25."},"ddc":["004"],"status":"public","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"doi":"10.1145/3371093","year":"2020","language":[{"iso":"eng"}],"oa":1,"intvolume":"         4","volume":4,"publication":"Proceedings of the ACM on Programming Languages","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","arxiv":1,"day":"01","publication_identifier":{"eissn":["2475-1421"]},"publisher":"ACM","file":[{"checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"access_level":"open_access","file_id":"8328","relation":"main_file","creator":"cziletti","date_created":"2020-09-01T11:12:58Z","date_updated":"2020-09-01T11:12:58Z","file_name":"2019_ACM_POPL_Wang.pdf","content_type":"application/pdf","file_size":564151}],"scopus_import":"1","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","quality_controlled":"1","author":[{"first_name":"Peixin","last_name":"Wang","full_name":"Wang, Peixin"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Deng, Yuxin","last_name":"Deng","first_name":"Yuxin"},{"last_name":"Xu","full_name":"Xu, Ming","first_name":"Ming"}],"file_date_updated":"2020-09-01T11:12:58Z","_id":"8324","date_created":"2020-08-30T22:01:12Z"},{"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","issue":"9","fulldoi":"https://doi.org/10.1007/s00220-020-03828-8","date_updated":"2025-07-10T11:57:03Z","article_processing_charge":"No","department":[{"_id":"TaHa"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"doi":"10.1007/s00220-020-03828-8","isi":1,"date_published":"2020-09-01T00:00:00Z","citation":{"short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” <i>Communications in Mathematical Physics</i>, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-020-03828-8\">https://doi.org/10.1007/s00220-020-03828-8</a>.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. <i>Communications in Mathematical Physics</i>. 2020;378(9):1649-1675. doi:<a href=\"https://doi.org/10.1007/s00220-020-03828-8\">10.1007/s00220-020-03828-8</a>","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” <i>Communications in Mathematical Physics</i>, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:<a href=\"https://doi.org/10.1007/s00220-020-03828-8\">10.1007/s00220-020-03828-8</a>.","apa":"Kalinin, N., &#38; Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-020-03828-8\">https://doi.org/10.1007/s00220-020-03828-8</a>"},"oa_version":"Preprint","type":"journal_article","external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"month":"09","abstract":[{"lang":"eng","text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. "}],"acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","arxiv":1,"day":"01","publication":"Communications in Mathematical Physics","volume":378,"oa":1,"intvolume":"       378","year":"2020","language":[{"iso":"eng"}],"page":"1649-1675","_id":"8325","date_created":"2020-08-30T22:01:13Z","title":"Sandpile solitons via smoothing of superharmonic functions","quality_controlled":"1","author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","full_name":"Shkolnikov, Mikhail"}],"article_type":"original","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"publisher":"Springer Nature","scopus_import":"1"},{"date_updated":"2026-06-18T19:32:35Z","fulldoi":"https://doi.org/10.1002/anie.202008253","issue":"51","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"StFr"}],"article_processing_charge":"No","ddc":["540"],"citation":{"apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202008253\">https://doi.org/10.1002/anie.202008253</a>","mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” <i>Angewandte Chemie International Edition</i>, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:<a href=\"https://doi.org/10.1002/anie.202008253\">10.1002/anie.202008253</a>.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. <i>Angewandte Chemie International Edition</i>. 2020;59(51):22943-22946. doi:<a href=\"https://doi.org/10.1002/anie.202008253\">10.1002/anie.202008253</a>","ista":"Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946.","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/anie.202008253\">https://doi.org/10.1002/anie.202008253</a>.","ieee":"W. Schlemmer <i>et al.</i>, “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” <i>Angewandte Chemie International Edition</i>, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020.","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946."},"date_published":"2020-12-14T00:00:00Z","doi":"10.1002/anie.202008253","isi":1,"main_file_link":[{"url":"https://doi.org/10.1002/anie.202008253","open_access":"1"}],"status":"public","related_material":{"record":[{"status":"public","id":"9780","relation":"research_data"}]},"abstract":[{"lang":"eng","text":"We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles."}],"month":"12","type":"journal_article","external_id":{"isi":["000576148700001"]},"oa_version":"Published Version","volume":59,"publication":"Angewandte Chemie International Edition","day":"14","acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","language":[{"iso":"eng"}],"year":"2020","intvolume":"        59","oa":1,"page":"22943-22946","_id":"8329","date_created":"2020-09-03T16:10:56Z","scopus_import":"1","publisher":"Wiley","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"author":[{"last_name":"Schlemmer","full_name":"Schlemmer, Werner","first_name":"Werner"},{"last_name":"Nothdurft","full_name":"Nothdurft, Philipp","first_name":"Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"last_name":"Frühwirt","full_name":"Frühwirt, Philipp","first_name":"Philipp"},{"first_name":"Max","full_name":"Schmallegger, Max","last_name":"Schmallegger"},{"first_name":"Georg","full_name":"Gescheidt-Demner, Georg","last_name":"Gescheidt-Demner"},{"first_name":"Roland","full_name":"Fischer, Roland","last_name":"Fischer"},{"first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Kern","full_name":"Kern, Wolfgang","first_name":"Wolfgang"},{"first_name":"Stefan","last_name":"Spirk","full_name":"Spirk, Stefan"}],"article_type":"original","quality_controlled":"1","title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries"},{"day":"03","degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher","corr_author":"1","year":"2020","supervisor":[{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"oa":1,"_id":"8332","page":"120","date_created":"2020-09-04T12:24:12Z","file_date_updated":"2020-09-04T13:00:17Z","file":[{"file_size":1348815,"content_type":"application/pdf","date_created":"2020-09-04T12:17:47Z","date_updated":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf","checksum":"26fe261550f691280bda4c454bf015c7","creator":"bkragl","relation":"main_file","file_id":"8333","access_level":"open_access"},{"checksum":"b9694ce092b7c55557122adba8337ebc","creator":"bkragl","relation":"source_file","access_level":"closed","file_id":"8335","file_size":372312,"file_name":"kragl-thesis.zip","date_updated":"2020-09-04T13:00:17Z","date_created":"2020-09-04T13:00:17Z","content_type":"application/zip"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Bernhard","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87"}],"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","date_updated":"2026-06-18T19:29:42Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:8332","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"ToHe"}],"has_accepted_license":"1","article_processing_charge":"No","ddc":["000"],"citation":{"mla":"Kragl, Bernhard. <i>Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8332\">10.15479/AT:ISTA:8332</a>.","apa":"Kragl, B. (2020). <i>Verifying concurrent programs: Refinement, synchronization, sequentialization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8332\">https://doi.org/10.15479/AT:ISTA:8332</a>","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8332\">https://doi.org/10.15479/AT:ISTA:8332</a>.","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8332\">10.15479/AT:ISTA:8332</a>","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020."},"date_published":"2020-09-03T00:00:00Z","doi":"10.15479/AT:ISTA:8332","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8195"},{"relation":"part_of_dissertation","status":"public","id":"133"},{"status":"public","id":"160","relation":"part_of_dissertation"},{"status":"public","id":"8012","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step."}],"month":"09","type":"dissertation","oa_version":"Published Version"},{"publication":"Nature Communications","volume":11,"day":"27","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","language":[{"iso":"eng"}],"corr_author":"1","year":"2020","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"intvolume":"        11","oa":1,"_id":"8336","date_created":"2020-09-06T22:01:12Z","file_date_updated":"2020-09-10T08:05:19Z","scopus_import":"1","file":[{"checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"8357","file_size":3455704,"file_name":"2020_NatureComm_Kubiasova.pdf","date_created":"2020-09-10T08:05:19Z","date_updated":"2020-09-10T08:05:19Z","content_type":"application/pdf"}],"publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","author":[{"last_name":"Kubiasova","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","full_name":"Kubiasova, Karolina","orcid":"0000-0001-5630-9419","first_name":"Karolina"},{"full_name":"Montesinos López, Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","first_name":"Juan C"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"first_name":"Jaroslav","full_name":"Nisler, Jaroslav","last_name":"Nisler"},{"first_name":"Václav","full_name":"Mik, Václav","last_name":"Mik"},{"full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana"},{"first_name":"Lucie","last_name":"Plíhalová","full_name":"Plíhalová, Lucie"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"full_name":"Marhavý, Peter","last_name":"Marhavý","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","first_name":"Peter"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"first_name":"David","last_name":"Zalabák","full_name":"Zalabák, David"},{"first_name":"Karel","full_name":"Berka, Karel","last_name":"Berka"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"first_name":"Petr","last_name":"Galuszka","full_name":"Galuszka, Petr"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ondřej","last_name":"Plíhal","full_name":"Plíhal, Ondřej"},{"first_name":"Lukáš","last_name":"Spíchal","full_name":"Spíchal, Lukáš"}],"quality_controlled":"1","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","date_updated":"2026-04-02T14:35:13Z","fulldoi":"https://doi.org/10.1038/s41467-020-17949-0","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"article_number":"4285","pmid":1,"department":[{"_id":"EvBe"}],"has_accepted_license":"1","article_processing_charge":"No","ddc":["580"],"citation":{"apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17949-0\">https://doi.org/10.1038/s41467-020-17949-0</a>","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” <i>Nature Communications</i>, vol. 11, 4285, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17949-0\">10.1038/s41467-020-17949-0</a>.","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17949-0\">10.1038/s41467-020-17949-0</a>","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17949-0\">https://doi.org/10.1038/s41467-020-17949-0</a>.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ieee":"K. Kubiasova <i>et al.</i>, “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2020-08-27T00:00:00Z","isi":1,"doi":"10.1038/s41467-020-17949-0","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"status":"public","abstract":[{"text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.","lang":"eng"}],"month":"08","type":"journal_article","external_id":{"isi":["000567931000002"],"pmid":["32855390"]},"oa_version":"Published Version"},{"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"status":"public","isi":1,"doi":"10.1038/s41467-020-17700-9","date_published":"2020-08-27T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>","ieee":"I. Antoniadi <i>et al.</i>, “Cell-surface receptors enable perception of extracellular cytokinins,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>, vol. 11, 4284, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>.","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>"},"ddc":["580"],"oa_version":"Published Version","type":"journal_article","external_id":{"pmid":["32855409"],"isi":["000567931000001"]},"month":"08","abstract":[{"text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.","lang":"eng"}],"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","fulldoi":"https://doi.org/10.1038/s41467-020-17700-9","date_updated":"2026-04-03T09:25:48Z","article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"JiFr"}],"pmid":1,"article_number":"4284","file_date_updated":"2020-12-10T12:23:56Z","date_created":"2020-09-06T22:01:13Z","_id":"8337","title":"Cell-surface receptors enable perception of extracellular cytokinins","quality_controlled":"1","article_type":"original","author":[{"first_name":"Ioanna","full_name":"Antoniadi, Ioanna","last_name":"Antoniadi"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","full_name":"Gelová, Zuzana","first_name":"Zuzana","orcid":"0000-0003-4783-1752"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"first_name":"Ondřej","last_name":"Plíhal","full_name":"Plíhal, Ondřej"},{"first_name":"Radim","full_name":"Simerský, Radim","last_name":"Simerský"},{"first_name":"Václav","full_name":"Mik, Václav","last_name":"Mik"},{"last_name":"Vain","full_name":"Vain, Thomas","first_name":"Thomas"},{"first_name":"Eduardo","full_name":"Mateo-Bonmatí, Eduardo","last_name":"Mateo-Bonmatí"},{"full_name":"Karady, Michal","last_name":"Karady","first_name":"Michal"},{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"first_name":"Lenka","last_name":"Plačková","full_name":"Plačková, Lenka"},{"first_name":"Korawit","full_name":"Opassathian, Korawit","last_name":"Opassathian"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Karel","full_name":"Doležal, Karel","last_name":"Doležal"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"last_name":"Turnbull","full_name":"Turnbull, Colin","first_name":"Colin"}],"publication_identifier":{"eissn":["2041-1723"]},"publisher":"Springer Nature","file":[{"access_level":"open_access","file_id":"8936","relation":"main_file","creator":"dernst","checksum":"5b96f39b598de7510cfefefb819b9a6d","success":1,"date_created":"2020-12-10T12:23:56Z","file_name":"2020_NatureComm_Antoniadi.pdf","date_updated":"2020-12-10T12:23:56Z","content_type":"application/pdf","file_size":3526415}],"scopus_import":"1","acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","day":"27","volume":11,"publication":"Nature Communications","oa":1,"intvolume":"        11","acknowledged_ssus":[{"_id":"Bio"}],"year":"2020","language":[{"iso":"eng"}]},{"date_updated":"2026-04-16T09:32:27Z","fulldoi":"https://doi.org/10.1007/978-3-030-45374-9_21","publication_status":"published","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"article_processing_charge":"No","isi":1,"doi":"10.1007/978-3-030-45374-9_21","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/337"}],"status":"public","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"citation":{"mla":"Genise, Nicholas, et al. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, vol. 12110, Springer Nature, 2020, pp. 623–51, doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">10.1007/978-3-030-45374-9_21</a>.","apa":"Genise, N., Micciancio, D., Peikert, C., &#38; Walter, M. (2020). Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i> (Vol. 12110, pp. 623–651). Edinburgh, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">https://doi.org/10.1007/978-3-030-45374-9_21</a>","ama":"Genise N, Micciancio D, Peikert C, Walter M. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In: <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>. Vol 12110. Springer Nature; 2020:623-651. doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">10.1007/978-3-030-45374-9_21</a>","chicago":"Genise, Nicholas, Daniele Micciancio, Chris Peikert, and Michael Walter. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” In <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, 12110:623–51. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">https://doi.org/10.1007/978-3-030-45374-9_21</a>.","ista":"Genise N, Micciancio D, Peikert C, Walter M. 2020. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography, LNCS, vol. 12110, 623–651.","short":"N. Genise, D. Micciancio, C. Peikert, M. Walter, in:, 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography, Springer Nature, 2020, pp. 623–651.","ieee":"N. Genise, D. Micciancio, C. Peikert, and M. Walter, “Improved discrete Gaussian and subgaussian analysis for lattice cryptography,” in <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, Edinburgh, United Kingdom, 2020, vol. 12110, pp. 623–651."},"date_published":"2020-05-15T00:00:00Z","external_id":{"isi":["001299210200021"]},"type":"conference","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend.\r\nIn this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach.\r\nAs a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems."}],"month":"05","day":"15","volume":12110,"publication":"23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography","intvolume":"     12110","oa":1,"conference":{"start_date":"2020-05-04","end_date":"2020-05-07","location":"Edinburgh, United Kingdom","name":"PKC: Public-Key Cryptography"},"language":[{"iso":"eng"}],"year":"2020","_id":"8339","page":"623-651","date_created":"2020-09-06T22:01:13Z","author":[{"last_name":"Genise","full_name":"Genise, Nicholas","first_name":"Nicholas"},{"last_name":"Micciancio","full_name":"Micciancio, Daniele","first_name":"Daniele"},{"last_name":"Peikert","full_name":"Peikert, Chris","first_name":"Chris"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","full_name":"Walter, Michael","first_name":"Michael","orcid":"0000-0003-3186-2482"}],"quality_controlled":"1","title":"Improved discrete Gaussian and subgaussian analysis for lattice cryptography","scopus_import":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030453732"]}},{"day":"08","degree_awarded":"PhD","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","language":[{"iso":"eng"}],"corr_author":"1","OA_place":"publisher","year":"2020","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"supervisor":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"oa":1,"_id":"8341","date_created":"2020-09-08T08:53:53Z","page":"215","file_date_updated":"2021-09-16T12:49:12Z","file":[{"creator":"dernst","relation":"source_file","file_id":"8342","access_level":"closed","checksum":"70871b335a595252a66c6bbf0824fb02","file_size":65246782,"content_type":"application/x-zip-compressed","date_created":"2020-09-08T09:00:29Z","date_updated":"2021-09-16T12:49:12Z","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip"},{"file_size":31259058,"content_type":"application/pdf","date_updated":"2021-09-16T12:49:12Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf","date_created":"2020-09-08T09:00:27Z","checksum":"59a62275088b00b7241e6ff4136434c7","creator":"dernst","relation":"main_file","file_id":"8343","access_level":"open_access"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"author":[{"orcid":"0000-0003-1365-5631","first_name":"Urban","last_name":"Bezeljak","full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"}],"title":"In vitro reconstitution of a Rab activation switch","date_updated":"2026-04-08T07:24:56Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:8341","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","alternative_title":["ISTA Thesis"],"department":[{"_id":"MaLo"}],"has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"citation":{"apa":"Bezeljak, U. (2020). <i>In vitro reconstitution of a Rab activation switch</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>","mla":"Bezeljak, Urban. <i>In Vitro Reconstitution of a Rab Activation Switch</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020."},"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"date_published":"2020-09-08T00:00:00Z","doi":"10.15479/AT:ISTA:8341","status":"public","abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"related_material":{"record":[{"id":"7580","status":"public","relation":"part_of_dissertation"}]},"month":"09","type":"dissertation","oa_version":"Published Version"},{"oa":1,"supervisor":[{"first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","corr_author":"1","language":[{"iso":"eng"}],"year":"2020","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"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.","degree_awarded":"PhD","day":"09","author":[{"orcid":"0000-0003-0493-3775","first_name":"Julia","last_name":"Steiner","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","full_name":"Steiner, Julia"}],"title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","file":[{"checksum":"2388d7e6e7a4d364c096fa89f305c3de","creator":"jsteiner","relation":"main_file","access_level":"open_access","file_id":"8354","file_size":117547589,"date_created":"2020-09-09T14:22:35Z","file_name":"Thesis_Julia_Steiner_pdfA.pdf","date_updated":"2021-09-16T12:40:56Z","content_type":"application/pdf"},{"file_name":"Thesis_Julia_Steiner.docx","date_updated":"2020-09-15T08:48:37Z","date_created":"2020-09-09T14:23:25Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":223328668,"checksum":"ba112f957b7145462d0ab79044873ee9","access_level":"closed","file_id":"8355","creator":"jsteiner","relation":"source_file"}],"publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-16T12:40:56Z","page":"191","_id":"8353","date_created":"2020-09-09T14:27:01Z","department":[{"_id":"LeSa"}],"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","date_updated":"2026-04-08T07:23:36Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:8353","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","oa_version":"None","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8284"}]},"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","doi":"10.15479/AT:ISTA:8353","status":"public","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"citation":{"short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>","ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","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>.","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>.","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>"},"ddc":["572"],"date_published":"2020-09-09T00:00:00Z"}]