[{"oa":1,"oa_version":"Preprint","date_updated":"2021-01-12T08:19:02Z","month":"09","main_file_link":[{"url":"https://doi.org/10.1101/2020.06.08.140772","open_access":"1"}],"date_published":"2020-09-17T00:00:00Z","type":"preprint","year":"2020","language":[{"iso":"eng"}],"title":"Structural basis of client specificity in mitochondrial membrane-protein chaperones","publication":"bioRxiv","extern":"1","author":[{"last_name":"Sučec","first_name":"Iva","full_name":"Sučec, Iva"},{"first_name":"Yong","full_name":"Wang, Yong","last_name":"Wang"},{"full_name":"Dakhlaoui, Ons","first_name":"Ons","last_name":"Dakhlaoui"},{"last_name":"Weinhäupl","first_name":"Katharina","full_name":"Weinhäupl, Katharina"},{"last_name":"Jores","first_name":"Tobias","full_name":"Jores, Tobias"},{"first_name":"Doriane","full_name":"Costa, Doriane","last_name":"Costa"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"first_name":"Martha","full_name":"Brennich, Martha","last_name":"Brennich"},{"full_name":"Rapaport, Doron","first_name":"Doron","last_name":"Rapaport"},{"full_name":"Lindorff-Larsen, Kresten","first_name":"Kresten","last_name":"Lindorff-Larsen"},{"last_name":"Bersch","full_name":"Bersch, Beate","first_name":"Beate"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"_id":"8403","date_created":"2020-09-17T10:27:47Z","publisher":"Cold Spring Harbor Laboratory","publication_status":"submitted","day":"17","citation":{"chicago":"Sučec, Iva, Yong Wang, Ons Dakhlaoui, Katharina Weinhäupl, Tobias Jores, Doriane Costa, Audrey Hessel, et al. “Structural Basis of Client Specificity in Mitochondrial Membrane-Protein Chaperones.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.06.08.140772\">https://doi.org/10.1101/2020.06.08.140772</a>.","ieee":"I. Sučec <i>et al.</i>, “Structural basis of client specificity in mitochondrial membrane-protein chaperones,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","apa":"Sučec, I., Wang, Y., Dakhlaoui, O., Weinhäupl, K., Jores, T., Costa, D., … Schanda, P. (n.d.). Structural basis of client specificity in mitochondrial membrane-protein chaperones. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.06.08.140772\">https://doi.org/10.1101/2020.06.08.140772</a>","ama":"Sučec I, Wang Y, Dakhlaoui O, et al. Structural basis of client specificity in mitochondrial membrane-protein chaperones. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.06.08.140772\">10.1101/2020.06.08.140772</a>","mla":"Sučec, Iva, et al. “Structural Basis of Client Specificity in Mitochondrial Membrane-Protein Chaperones.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.06.08.140772\">10.1101/2020.06.08.140772</a>.","ista":"Sučec I, Wang Y, Dakhlaoui O, Weinhäupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B, Schanda P. Structural basis of client specificity in mitochondrial membrane-protein chaperones. bioRxiv, <a href=\"https://doi.org/10.1101/2020.06.08.140772\">10.1101/2020.06.08.140772</a>.","short":"I. Sučec, Y. Wang, O. Dakhlaoui, K. Weinhäupl, T. Jores, D. Costa, A. Hessel, M. Brennich, D. Rapaport, K. Lindorff-Larsen, B. Bersch, P. Schanda, BioRxiv (n.d.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"text":"Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding of how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity <jats:italic>vs.</jats:italic> specificity.","lang":"eng"}],"doi":"10.1101/2020.06.08.140772","status":"public"},{"citation":{"short":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, P. Schanda, BioRxiv (n.d.).","ista":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. bioRxiv, <a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>.","mla":"Weinhäupl, Katharina, et al. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>.","ama":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.03.13.990150\">10.1101/2020.03.13.990150</a>","apa":"Weinhäupl, K., Wang, Y., Hessel, A., Brennich, M., Lindorff-Larsen, K., &#38; Schanda, P. (n.d.). Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.03.13.990150\">https://doi.org/10.1101/2020.03.13.990150</a>","ieee":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, and P. Schanda, “Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Weinhäupl, Katharina, Yong Wang, Audrey Hessel, Martha Brennich, Kresten Lindorff-Larsen, and Paul Schanda. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.03.13.990150\">https://doi.org/10.1101/2020.03.13.990150</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.1101/2020.03.13.990150","article_processing_charge":"No","abstract":[{"text":"<jats:p>The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX<jats:sub>3</jats:sub>C-X<jats:sub><jats:italic>n</jats:italic></jats:sub>-CX<jats:sub>3</jats:sub>C motifs are formed, short marginally stable <jats:italic>α</jats:italic>-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles.</jats:p>","lang":"eng"}],"author":[{"full_name":"Weinhäupl, Katharina","first_name":"Katharina","last_name":"Weinhäupl"},{"last_name":"Wang","first_name":"Yong","full_name":"Wang, Yong"},{"last_name":"Hessel","first_name":"Audrey","full_name":"Hessel, Audrey"},{"first_name":"Martha","full_name":"Brennich, Martha","last_name":"Brennich"},{"full_name":"Lindorff-Larsen, Kresten","first_name":"Kresten","last_name":"Lindorff-Larsen"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"}],"_id":"8404","publication_status":"submitted","date_created":"2020-09-17T10:27:59Z","publisher":"Cold Spring Harbor Laboratory","extern":"1","day":"14","language":[{"iso":"eng"}],"publication":"bioRxiv","title":"Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone","year":"2020","type":"preprint","main_file_link":[{"url":"https://doi.org/10.1101/2020.03.13.990150","open_access":"1"}],"date_published":"2020-03-14T00:00:00Z","date_updated":"2021-01-12T08:19:03Z","month":"03","oa_version":"Preprint","oa":1},{"oa_version":"None","publication_identifier":{"isbn":["9-780-6912-0253-2"]},"page":"224","alternative_title":["Annals of Mathematics Studies"],"date_published":"2020-03-01T00:00:00Z","date_updated":"2021-12-21T10:50:49Z","month":"03","intvolume":"       208","language":[{"iso":"eng"}],"edition":"1","title":"Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom","type":"book","year":"2020","citation":{"ama":"Kaloshin V, Zhang K. <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>. Vol 208. 1st ed. Princeton University Press; 2020. doi:<a href=\"https://doi.org/10.1515/9780691204932\">10.1515/9780691204932</a>","mla":"Kaloshin, Vadim, and Ke Zhang. <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>. 1st ed., vol. 208, Princeton University Press, 2020, doi:<a href=\"https://doi.org/10.1515/9780691204932\">10.1515/9780691204932</a>.","short":"V. Kaloshin, K. Zhang, Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom, 1st ed., Princeton University Press, 2020.","ista":"Kaloshin V, Zhang K. 2020. Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom 1st ed., Princeton University Press, 224p.","chicago":"Kaloshin, Vadim, and Ke Zhang. <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>. 1st ed. Vol. 208. AMS. Princeton University Press, 2020. <a href=\"https://doi.org/10.1515/9780691204932\">https://doi.org/10.1515/9780691204932</a>.","ieee":"V. Kaloshin and K. Zhang, <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i>, 1st ed., vol. 208. Princeton University Press, 2020.","apa":"Kaloshin, V., &#38; Zhang, K. (2020). <i>Arnold Diffusion for Smooth Systems of Two and a Half Degrees of Freedom</i> (1st ed., Vol. 208). Princeton University Press. <a href=\"https://doi.org/10.1515/9780691204932\">https://doi.org/10.1515/9780691204932</a>"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1515/9780691204932","status":"public","article_processing_charge":"No","volume":208,"abstract":[{"lang":"eng","text":"Arnold diffusion, which concerns the appearance of chaos in classical mechanics, is one of the most important problems in the fields of dynamical systems and mathematical physics. Since it was discovered by Vladimir Arnold in 1963, it has attracted the efforts of some of the most prominent researchers in mathematics. The question is whether a typical perturbation of a particular system will result in chaotic or unstable dynamical phenomena. In this groundbreaking book, Vadim Kaloshin and Ke Zhang provide the first complete proof of Arnold diffusion, demonstrating that that there is topological instability for typical perturbations of five-dimensional integrable systems (two and a half degrees of freedom).\r\nThis proof realizes a plan John Mather announced in 2003 but was unable to complete before his death. Kaloshin and Zhang follow Mather’s strategy but emphasize a more Hamiltonian approach, tying together normal forms theory, hyperbolic theory, Mather theory, and weak KAM theory. Offering a complete, clean, and modern explanation of the steps involved in the proof, and a clear account of background material, this book is designed to be accessible to students as well as researchers. The result is a critical contribution to mathematical physics and dynamical systems, especially Hamiltonian systems."}],"publication_status":"published","_id":"8414","date_created":"2020-09-17T10:41:05Z","publisher":"Princeton University Press","author":[{"first_name":"Vadim","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Zhang","full_name":"Zhang, Ke","first_name":"Ke"}],"extern":"1","scopus_import":"1","quality_controlled":"1","series_title":"AMS","day":"01"},{"department":[{"_id":"KrCh"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771597"]},"license":"https://creativecommons.org/licenses/by/3.0/","intvolume":"       170","alternative_title":["LIPIcs"],"article_number":"22:1-22:13","date_published":"2020-08-18T00:00:00Z","arxiv":1,"year":"2020","type":"conference","publication":"45th International Symposium on Mathematical Foundations of Computer Science","title":"Simplified game of life: Algorithms and complexity","file":[{"access_level":"open_access","file_id":"8550","success":1,"creator":"dernst","file_size":491374,"relation":"main_file","file_name":"2020_LIPIcs_Chatterjee.pdf","checksum":"bbd7c4f55d45f2ff2a0a4ef0e10a77b1","date_created":"2020-09-21T13:57:34Z","date_updated":"2020-09-21T13:57:34Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"date_created":"2020-09-20T22:01:36Z","status":"public","volume":170,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Simplified Game of Life: Algorithms and Complexity.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 22:1-22:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. Simplified game of life: Algorithms and complexity. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">10.4230/LIPIcs.MFCS.2020.22</a>","ista":"Chatterjee K, Ibsen-Jensen R, Jecker IR, Svoboda J. 2020. Simplified game of life: Algorithms and complexity. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 22:1-22:13.","short":"K. Chatterjee, R. Ibsen-Jensen, I.R. Jecker, J. Svoboda, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Ismael R Jecker, and Jakub Svoboda. “Simplified Game of Life: Algorithms and Complexity.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., Jecker, I. R., &#38; Svoboda, J. (2020). Simplified game of life: Algorithms and complexity. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.22\">https://doi.org/10.4230/LIPIcs.MFCS.2020.22</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, I. R. Jecker, and J. Svoboda, “Simplified game of life: Algorithms and complexity,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170."},"oa":1,"oa_version":"Published Version","file_date_updated":"2020-09-21T13:57:34Z","month":"08","has_accepted_license":"1","date_updated":"2025-07-10T11:57:06Z","acknowledgement":"Krishnendu Chatterjee: The research was partially supported by the Vienna Science and\r\nTechnology Fund (WWTF) Project ICT15-003.\r\nIsmaël Jecker: This project has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","ddc":["000"],"ec_funded":1,"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"conference":{"end_date":"2020-08-28","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2020-08-24","location":"Prague, Czech Republic"},"day":"18","_id":"8533","external_id":{"arxiv":["2007.02894"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","last_name":"Jecker","first_name":"Ismael R","full_name":"Jecker, Ismael R"},{"orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub","first_name":"Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"}],"publication_status":"published","doi":"10.4230/LIPIcs.MFCS.2020.22","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Game of Life is a simple and elegant model to study dynamical system over networks. The model consists of a graph where every vertex has one of two types, namely, dead or alive. A configuration is a mapping of the vertices to the types. An update rule describes how the type of a vertex is updated given the types of its neighbors. In every round, all vertices are updated synchronously, which leads to a configuration update. While in general, Game of Life allows a broad range of update rules, we focus on two simple families of update rules, namely, underpopulation and overpopulation, that model several interesting dynamics studied in the literature. In both settings, a dead vertex requires at least a desired number of live neighbors to become alive. For underpopulation (resp., overpopulation), a live vertex requires at least (resp. at most) a desired number of live neighbors to remain alive. We study the basic computation problems, e.g., configuration reachability, for these two families of rules. For underpopulation rules, we show that these problems can be solved in polynomial time, whereas for overpopulation rules they are PSPACE-complete."}]},{"file_date_updated":"2020-09-21T14:17:08Z","oa_version":"Published Version","oa":1,"acknowledgement":"Ismaël Jecker: This project has received funding from the European Union’s Horizon\r\n2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.\r\n754411. Nicolas Mazzocchi: PhD fellowship FRIA from the F.R.S.-FNRS.","month":"08","has_accepted_license":"1","date_updated":"2025-07-10T11:57:07Z","ec_funded":1,"ddc":["000"],"doi":"10.4230/LIPIcs.MFCS.2020.51","article_processing_charge":"No","abstract":[{"lang":"eng","text":"A regular language L of finite words is composite if there are regular languages L₁,L₂,…,L_t such that L = ⋂_{i = 1}^t L_i and the index (number of states in a minimal DFA) of every language L_i is strictly smaller than the index of L. Otherwise, L is prime. Primality of regular languages was introduced and studied in [O. Kupferman and J. Mosheiff, 2015], where the complexity of deciding the primality of the language of a given DFA was left open, with a doubly-exponential gap between the upper and lower bounds. We study primality for unary regular languages, namely regular languages with a singleton alphabet. A unary language corresponds to a subset of ℕ, making the study of unary prime languages closer to that of primality in number theory. We show that the setting of languages is richer. In particular, while every composite number is the product of two smaller numbers, the number t of languages necessary to decompose a composite unary language induces a strict hierarchy. In addition, a primality witness for a unary language L, namely a word that is not in L but is in all products of languages that contain L and have an index smaller than L’s, may be of exponential length. Still, we are able to characterize compositionality by structural properties of a DFA for L, leading to a LogSpace algorithm for primality checking of unary DFAs."}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2020-08-24","location":"Prague, Czech Republic","end_date":"2020-08-28"},"day":"18","_id":"8534","publication_status":"published","author":[{"last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","full_name":"Jecker, Ismael R","first_name":"Ismael R"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"},{"full_name":"Mazzocchi, Nicolas","first_name":"Nicolas","last_name":"Mazzocchi"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_identifier":{"isbn":["9783959771597"],"issn":["1868-8969"]},"department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"article_number":"51:1-51:12","date_published":"2020-08-18T00:00:00Z","intvolume":"       170","publication":"45th International Symposium on Mathematical Foundations of Computer Science","corr_author":"1","title":"Unary prime languages","file":[{"checksum":"2dc9e2fad6becd4563aef3e27a473f70","file_name":"2020_LIPIcsMFCS_Jecker.pdf","relation":"main_file","file_size":597977,"content_type":"application/pdf","date_updated":"2020-09-21T14:17:08Z","date_created":"2020-09-21T14:17:08Z","success":1,"access_level":"open_access","file_id":"8552","creator":"dernst"}],"language":[{"iso":"eng"}],"year":"2020","type":"conference","status":"public","volume":170,"citation":{"ama":"Jecker IR, Kupferman O, Mazzocchi N. Unary prime languages. In: <i>45th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>","mla":"Jecker, Ismael R., et al. “Unary Prime Languages.” <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 170, 51:1-51:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">10.4230/LIPIcs.MFCS.2020.51</a>.","short":"I.R. Jecker, O. Kupferman, N. Mazzocchi, in:, 45th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ista":"Jecker IR, Kupferman O, Mazzocchi N. 2020. Unary prime languages. 45th International Symposium on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 170, 51:1-51:12.","chicago":"Jecker, Ismael R, Orna Kupferman, and Nicolas Mazzocchi. “Unary Prime Languages.” In <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 170. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>.","ieee":"I. R. Jecker, O. Kupferman, and N. Mazzocchi, “Unary prime languages,” in <i>45th International Symposium on Mathematical Foundations of Computer Science</i>, Prague, Czech Republic, 2020, vol. 170.","apa":"Jecker, I. R., Kupferman, O., &#38; Mazzocchi, N. (2020). Unary prime languages. In <i>45th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 170). Prague, Czech Republic: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2020.51\">https://doi.org/10.4230/LIPIcs.MFCS.2020.51</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"date_created":"2020-09-20T22:01:36Z"},{"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176 and Marie SkłodowskaCurie Grant Agreement No. 665385.","month":"07","has_accepted_license":"1","date_updated":"2026-04-16T08:26:38Z","file_date_updated":"2020-09-21T07:51:44Z","oa_version":"Published Version","oa":1,"article_type":"original","doi":"10.1145/3386569.3392466","abstract":[{"lang":"eng","text":"We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation."}],"article_processing_charge":"No","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"day":"08","external_id":{"isi":["000583700300038"]},"_id":"8535","author":[{"first_name":"Tomas","full_name":"Skrivan, Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Soderstrom","first_name":"Andreas","full_name":"Soderstrom, Andreas"},{"last_name":"Johansson","full_name":"Johansson, John","first_name":"John"},{"full_name":"Sprenger, Christoph","first_name":"Christoph","last_name":"Sprenger"},{"last_name":"Museth","full_name":"Museth, Ken","first_name":"Ken"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"publication_status":"published","publisher":"Association for Computing Machinery","ec_funded":1,"ddc":["000"],"article_number":"65","date_published":"2020-07-08T00:00:00Z","intvolume":"        39","isi":1,"department":[{"_id":"ChWo"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"status":"public","volume":39,"citation":{"mla":"Skrivan, Tomas, et al. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 65, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>.","ama":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392466\">10.1145/3386569.3392466</a>","short":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ista":"Skrivan T, Soderstrom A, Johansson J, Sprenger C, Museth K, Wojtan C. 2020. Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. ACM Transactions on Graphics. 39(4), 65.","chicago":"Skrivan, Tomas, Andreas Soderstrom, John Johansson, Christoph Sprenger, Ken Museth, and Chris Wojtan. “Wave Curves: Simulating Lagrangian Water Waves on Dynamically Deforming Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>.","apa":"Skrivan, T., Soderstrom, A., Johansson, J., Sprenger, C., Museth, K., &#38; Wojtan, C. (2020). Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392466\">https://doi.org/10.1145/3386569.3392466</a>","ieee":"T. Skrivan, A. Soderstrom, J. Johansson, C. Sprenger, K. Museth, and C. Wojtan, “Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","scopus_import":"1","date_created":"2020-09-20T22:01:37Z","publication":"ACM Transactions on Graphics","corr_author":"1","title":"Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces","file":[{"content_type":"application/pdf","date_created":"2020-09-21T07:51:44Z","date_updated":"2020-09-21T07:51:44Z","file_name":"2020_ACM_Skrivan.pdf","checksum":"c3a680893f01cc4a9e961ff0a4cfa12f","relation":"main_file","file_size":20223953,"creator":"dernst","success":1,"file_id":"8541","access_level":"open_access"}],"language":[{"iso":"eng"}],"type":"journal_article","year":"2020","issue":"4"},{"day":"01","conference":{"name":"ISIT: International Symposium on Information Theory","start_date":"2020-06-21","location":"Los Angeles, CA, United States","end_date":"2020-06-26"},"publication_status":"published","_id":"8536","external_id":{"isi":["000714963400069"],"arxiv":["1909.04892"]},"publisher":"IEEE","author":[{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco"},{"last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali"},{"full_name":"Cioffi, John","first_name":"John","last_name":"Cioffi"},{"last_name":"Goldsmith","first_name":"Andrea","full_name":"Goldsmith, Andrea"}],"doi":"10.1109/ISIT44484.2020.9174141","abstract":[{"text":"This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1.","lang":"eng"}],"article_processing_charge":"No","oa":1,"oa_version":"Preprint","month":"06","date_updated":"2025-09-10T10:27:05Z","acknowledgement":"M. Mondelli was partially supported by grants NSF DMS-1613091, CCF-1714305, IIS-1741162 and ONR N00014-18-1-2729. S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by Huawei.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.04892"}],"year":"2020","type":"conference","publication":"IEEE International Symposium on Information Theory - Proceedings","title":"Simplified successive cancellation decoding of polar codes has sublinear latency","language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"9047","relation":"later_version"}]},"date_created":"2020-09-20T22:01:37Z","status":"public","volume":"2020-June","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Mondelli, Marco, et al. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” <i>IEEE International Symposium on Information Theory - Proceedings</i>, vol. 2020–June, 401–406, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>.","ama":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. Simplified successive cancellation decoding of polar codes has sublinear latency. In: <i>IEEE International Symposium on Information Theory - Proceedings</i>. Vol 2020-June. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">10.1109/ISIT44484.2020.9174141</a>","short":"M. Mondelli, S.A. Hashemi, J. Cioffi, A. Goldsmith, in:, IEEE International Symposium on Information Theory - Proceedings, IEEE, 2020.","ista":"Mondelli M, Hashemi SA, Cioffi J, Goldsmith A. 2020. Simplified successive cancellation decoding of polar codes has sublinear latency. IEEE International Symposium on Information Theory - Proceedings. ISIT: International Symposium on Information Theory vol. 2020–June, 401–406.","chicago":"Mondelli, Marco, Seyyed Ali Hashemi, John Cioffi, and Andrea Goldsmith. “Simplified Successive Cancellation Decoding of Polar Codes Has Sublinear Latency.” In <i>IEEE International Symposium on Information Theory - Proceedings</i>, Vol. 2020–June. IEEE, 2020. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>.","apa":"Mondelli, M., Hashemi, S. A., Cioffi, J., &#38; Goldsmith, A. (2020). Simplified successive cancellation decoding of polar codes has sublinear latency. In <i>IEEE International Symposium on Information Theory - Proceedings</i> (Vol. 2020–June). Los Angeles, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/ISIT44484.2020.9174141\">https://doi.org/10.1109/ISIT44484.2020.9174141</a>","ieee":"M. Mondelli, S. A. Hashemi, J. Cioffi, and A. Goldsmith, “Simplified successive cancellation decoding of polar codes has sublinear latency,” in <i>IEEE International Symposium on Information Theory - Proceedings</i>, Los Angeles, CA, United States, 2020, vol. 2020–June."},"isi":1,"department":[{"_id":"MaMo"}],"publication_identifier":{"isbn":["9781728164328"],"issn":["2157-8095"]},"article_number":"401-406","date_published":"2020-06-01T00:00:00Z","arxiv":1},{"day":"01","external_id":{"isi":["000592182600004"],"arxiv":["1708.08013"]},"_id":"8539","publication_status":"published","publisher":"Société Mathématique de France","author":[{"last_name":"Su","full_name":"Su, C.","first_name":"C."},{"first_name":"Gufang","full_name":"Zhao, Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","last_name":"Zhao"},{"last_name":"Zhong","full_name":"Zhong, C.","first_name":"C."}],"doi":"10.24033/asens.2431","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions."},{"text":"Les bases stables cohomologiques et K-théoriques proviennent de l’étude de la cohomologie quantique et de la K-théorie quantique. La formule de restriction pour les bases stables cohomologiques a joué un rôle important dans le calcul de la connexion quantique du fibré cotangent de variétés de drapeaux partielles. Dans cet article, nous étudions les bases stables K-théoriques de fibré cotangents des variétés de drapeaux. Nous décrivons ces bases en fonction de l’action de l’algèbre de Hecke affine et de l’algèbre de Kostant-Kumar. En utilisant cette description algébrique et la méthode des polynômes de racine, nous donnons une formule de restriction des bases stables. Nous l’appliquons\r\npour obtenir la formule de restriction pour les variétés de drapeaux partielles. Nous construisons également une relation entre la base stable et la base de Casselman dans les représentations de la série principale du groupe dual de Langlands p-adique. Comme une application, nous donnons une formule close pour la matrice de transition entre la base de Casselman et les fonctions caractéristiques. ","lang":"fre"}],"article_type":"original","oa":1,"oa_version":"Preprint","month":"06","date_updated":"2023-08-22T09:27:57Z","main_file_link":[{"url":"https://arxiv.org/abs/1708.08013","open_access":"1"}],"year":"2020","issue":"3","type":"journal_article","publication":"Annales Scientifiques de l'Ecole Normale Superieure","title":"On the K-theory stable bases of the springer resolution","language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","date_created":"2020-09-20T22:01:38Z","status":"public","volume":53,"citation":{"apa":"Su, C., Zhao, G., &#38; Zhong, C. (2020). On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Société Mathématique de France. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>","ieee":"C. Su, G. Zhao, and C. Zhong, “On the K-theory stable bases of the springer resolution,” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3. Société Mathématique de France, pp. 663–671, 2020.","chicago":"Su, C., Gufang Zhao, and C. Zhong. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Société Mathématique de France, 2020. <a href=\"https://doi.org/10.24033/asens.2431\">https://doi.org/10.24033/asens.2431</a>.","short":"C. Su, G. Zhao, C. Zhong, Annales Scientifiques de l’Ecole Normale Superieure 53 (2020) 663–671.","ista":"Su C, Zhao G, Zhong C. 2020. On the K-theory stable bases of the springer resolution. Annales Scientifiques de l’Ecole Normale Superieure. 53(3), 663–671.","mla":"Su, C., et al. “On the K-Theory Stable Bases of the Springer Resolution.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 53, no. 3, Société Mathématique de France, 2020, pp. 663–71, doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>.","ama":"Su C, Zhao G, Zhong C. On the K-theory stable bases of the springer resolution. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. 2020;53(3):663-671. doi:<a href=\"https://doi.org/10.24033/asens.2431\">10.24033/asens.2431</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publication_identifier":{"issn":["0012-9593"]},"department":[{"_id":"TaHa"}],"intvolume":"        53","date_published":"2020-06-01T00:00:00Z","arxiv":1,"page":"663-671"},{"volume":39,"status":"public","citation":{"ieee":"K. Gavriil <i>et al.</i>, “Computational design of cold bent glass façades,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6. Association for Computing Machinery, 2020.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>","chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3414685.3417843\">https://doi.org/10.1145/3414685.3417843</a>.","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. <i>ACM Transactions on Graphics</i>. 2020;39(6). doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3414685.3417843\">10.1145/3414685.3417843</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/bend-dont-break/"}],"record":[{"status":"public","id":"8761","relation":"research_data"},{"status":"public","id":"8366","relation":"dissertation_contains"}]},"quality_controlled":"1","scopus_import":"1","date_created":"2020-09-23T11:30:02Z","title":"Computational design of cold bent glass façades","publication":"ACM Transactions on Graphics","corr_author":"1","language":[{"iso":"eng"}],"file":[{"creator":"bbickel","access_level":"open_access","file_id":"13084","success":1,"date_updated":"2023-05-23T20:54:43Z","date_created":"2023-05-23T20:54:43Z","content_type":"application/pdf","file_size":28964641,"relation":"main_file","checksum":"c7f67717ad74e670b7daeae732abe151","file_name":"coldglass.pdf"}],"issue":"6","type":"journal_article","year":"2020","article_number":"208","date_published":"2020-11-26T00:00:00Z","arxiv":1,"intvolume":"        39","department":[{"_id":"BeBi"}],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"isi":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","abstract":[{"text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface.","lang":"eng"}],"doi":"10.1145/3414685.3417843","day":"26","project":[{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"_id":"8562","publication_status":"published","author":[{"first_name":"Konstantinos","full_name":"Gavriil, Konstantinos","last_name":"Gavriil"},{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","first_name":"Ruslan"},{"last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus","first_name":"Jesus"},{"last_name":"Pellis","first_name":"Davide","full_name":"Pellis, Davide"},{"last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M","first_name":"Paul M"},{"first_name":"Florian","full_name":"Rist, Florian","last_name":"Rist"},{"last_name":"Pottmann","full_name":"Pottmann, Helmut","first_name":"Helmut"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"external_id":{"arxiv":["2009.03667"],"isi":["000595589100048"]},"publisher":"Association for Computing Machinery","ec_funded":1,"ddc":["000"],"acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","month":"11","date_updated":"2026-04-08T07:25:22Z","has_accepted_license":"1","file_date_updated":"2023-05-23T20:54:43Z","oa_version":"Submitted Version","article_type":"original","oa":1},{"has_accepted_license":"1","date_updated":"2026-04-07T08:37:11Z","month":"10","date_published":"2020-10-19T00:00:00Z","department":[{"_id":"JoCs"}],"oa":1,"contributor":[{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","contributor_type":"project_leader","orcid":"0000-0002-5193-4036"}],"file_date_updated":"2020-10-19T10:12:29Z","oa_version":"Published Version","_id":"8563","tmp":{"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","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2020-09-23T14:39:54Z","publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"},{"orcid":"0000-0002-1807-1929","full_name":"Gridchyn, Igor","first_name":"Igor","last_name":"Gridchyn","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","first_name":"Philipp","full_name":"Schönenberger, Philipp"}],"day":"19","related_material":{"record":[{"relation":"used_in_publication","id":"8740","status":"public"}]},"citation":{"apa":"Csicsvari, J. L., Gridchyn, I., &#38; Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","chicago":"Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">https://doi.org/10.15479/AT:ISTA:8563</a>.","short":"J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","mla":"Csicsvari, Jozsef L., et al. <i>Optogenetic Alteration of Hippocampal Network Activity</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8563\">10.15479/AT:ISTA:8563</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.15479/AT:ISTA:8563","article_processing_charge":"No","abstract":[{"text":"Supplementary data  provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife.","lang":"eng"}],"year":"2020","type":"research_data","ddc":["570"],"file":[{"file_id":"8564","access_level":"open_access","success":1,"creator":"jozsef","relation":"main_file","file_size":145243906,"file_name":"upload.tgz","checksum":"a16098a6d172f9c42ab5af5f6991668c","date_created":"2020-09-23T14:36:17Z","date_updated":"2020-09-23T14:36:17Z","content_type":"application/x-compressed"},{"file_size":11648,"relation":"main_file","checksum":"0bfc54b7e14c0694cd081617318ba606","file_name":"redme.docx","date_updated":"2020-10-19T10:12:29Z","date_created":"2020-10-19T10:12:29Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"open_access","file_id":"8675","success":1,"creator":"jozsef"}],"corr_author":"1","title":"Optogenetic alteration of hippocampal network activity"},{"has_accepted_license":"1","date_updated":"2025-06-12T06:58:51Z","month":"09","article_type":"original","oa":1,"oa_version":"Published Version","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"file_date_updated":"2020-09-28T13:16:15Z","author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"full_name":"Fitzek, Harald","first_name":"Harald","last_name":"Fitzek"},{"first_name":"Gerald","full_name":"Kothleitner, Gerald","last_name":"Kothleitner"},{"last_name":"Presser","full_name":"Presser, Volker","first_name":"Volker"},{"last_name":"Gollas","full_name":"Gollas, Bernhard","first_name":"Bernhard"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander"},{"last_name":"Abbas","first_name":"Qamar","full_name":"Abbas, Qamar"}],"_id":"8568","external_id":{"isi":["000573756600004"],"pmid":["32973214"]},"publication_status":"published","publisher":"Springer Nature","day":"24","doi":"10.1038/s41467-020-18610-6","article_processing_charge":"No","abstract":[{"text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.","lang":"eng"}],"ddc":["530"],"intvolume":"        11","article_number":"4838","date_published":"2020-09-24T00:00:00Z","isi":1,"publication_identifier":{"issn":["2041-1723"]},"department":[{"_id":"StFr"}],"date_created":"2020-09-25T07:23:13Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>","ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>.","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>"},"status":"public","volume":11,"type":"journal_article","year":"2020","pmid":1,"file":[{"creator":"dernst","access_level":"open_access","file_id":"8585","success":1,"date_updated":"2020-09-28T13:16:15Z","date_created":"2020-09-28T13:16:15Z","content_type":"application/pdf","relation":"main_file","file_size":1822469,"checksum":"eada7bc8dd16a49390137cff882ef328","file_name":"2020_NatureComm_Prehal.pdf"}],"language":[{"iso":"eng"}],"publication":"Nature Communications","corr_author":"1","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons"},{"intvolume":"        74","date_published":"2020-09-25T00:00:00Z","page":"49-75","department":[{"_id":"ToHe"}],"quality_controlled":"1","scopus_import":"1","date_created":"2020-09-26T14:41:29Z","status":"public","volume":74,"citation":{"chicago":"Geretti, Luca, Julien Alexandre Dit Sandretto, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Pieter Collins, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 74:49–75. EasyChair, 2020. <a href=\"https://doi.org/10.29007/zkf6\">https://doi.org/10.29007/zkf6</a>.","apa":"Geretti, L., Alexandre Dit Sandretto, J., Althoff, M., Benet, L., Chapoutot, A., Chen, X., … Schilling, C. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 74, pp. 49–75). EasyChair. <a href=\"https://doi.org/10.29007/zkf6\">https://doi.org/10.29007/zkf6</a>","ieee":"L. Geretti <i>et al.</i>, “ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, 2020, vol. 74, pp. 49–75.","mla":"Geretti, Luca, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 74, EasyChair, 2020, pp. 49–75, doi:<a href=\"https://doi.org/10.29007/zkf6\">10.29007/zkf6</a>.","ama":"Geretti L, Alexandre Dit Sandretto J, Althoff M, et al. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 74. EasyChair; 2020:49-75. doi:<a href=\"https://doi.org/10.29007/zkf6\">10.29007/zkf6</a>","ista":"Geretti L, Alexandre Dit Sandretto J, Althoff M, Benet L, Chapoutot A, Chen X, Collins P, Forets M, Freire D, Immler F, Kochdumper N, Sanders D, Schilling C. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 74, 49–75.","short":"L. Geretti, J. Alexandre Dit Sandretto, M. Althoff, L. Benet, A. Chapoutot, X. Chen, P. Collins, M. Forets, D. Freire, F. Immler, N. Kochdumper, D. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair, 2020, pp. 49–75."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","type":"conference","publication":"EPiC Series in Computing","corr_author":"1","title":"ARCH-COMP20 Category Report: Continuous and hybrid systems with nonlinear dynamics","language":[{"iso":"eng"}],"month":"09","date_updated":"2026-06-18T19:34:03Z","acknowledgement":"Christian Schilling acknowledges support in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411.","main_file_link":[{"url":"https://easychair.org/publications/download/nrdD","open_access":"1"}],"oa":1,"oa_version":"Published Version","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"conference":{"end_date":"2020-07-12","start_date":"2020-07-12","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"day":"25","_id":"8571","publication_status":"published","author":[{"full_name":"Geretti, Luca","first_name":"Luca","last_name":"Geretti"},{"last_name":"Alexandre Dit Sandretto","first_name":"Julien","full_name":"Alexandre Dit Sandretto, Julien"},{"last_name":"Althoff","full_name":"Althoff, Matthias","first_name":"Matthias"},{"last_name":"Benet","full_name":"Benet, Luis","first_name":"Luis"},{"last_name":"Chapoutot","full_name":"Chapoutot, Alexandre","first_name":"Alexandre"},{"last_name":"Chen","first_name":"Xin","full_name":"Chen, Xin"},{"last_name":"Collins","first_name":"Pieter","full_name":"Collins, Pieter"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"last_name":"Freire","first_name":"Daniel","full_name":"Freire, Daniel"},{"last_name":"Immler","full_name":"Immler, Fabian","first_name":"Fabian"},{"last_name":"Kochdumper","full_name":"Kochdumper, Niklas","first_name":"Niklas"},{"first_name":"David","full_name":"Sanders, David","last_name":"Sanders"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065"}],"publisher":"EasyChair","doi":"10.29007/zkf6","abstract":[{"lang":"eng","text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. This year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. These tools are applied to solve reachability analysis problems on six benchmark problems, two of them featuring hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools."}],"article_processing_charge":"No","ddc":["000"],"ec_funded":1},{"oa":1,"oa_version":"Published Version","month":"09","date_updated":"2026-06-18T19:34:29Z","acknowledgement":"The authors gratefully acknowledge financial support by the European Commission project\r\njustITSELF under grant number 817629, by the Austrian Science Fund (FWF) under grant\r\nZ211-N23 (Wittgenstein Award), by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411, and by the\r\nScience and Engineering Research Board (SERB) project with file number IMP/2018/000523.\r\nThis material is based upon work supported by the Air Force Office of Scientific Research under\r\naward number FA9550-19-1-0288. Any opinions, finding, and conclusions or recommendations\r\nexpressed in this material are those of the author(s) and do not necessarily reflect the views of\r\nthe United States Air Force.","main_file_link":[{"url":"https://easychair.org/publications/download/DRpS","open_access":"1"}],"ddc":["000"],"ec_funded":1,"project":[{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"day":"25","conference":{"end_date":"2020-07-12","start_date":"2020-07-12","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"_id":"8572","author":[{"full_name":"Althoff, Matthias","first_name":"Matthias","last_name":"Althoff"},{"first_name":"Stanley","full_name":"Bak, Stanley","last_name":"Bak"},{"full_name":"Bao, Zongnan","first_name":"Zongnan","last_name":"Bao"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"first_name":"Daniel","full_name":"Freire, Daniel","last_name":"Freire"},{"last_name":"Kochdumper","first_name":"Niklas","full_name":"Kochdumper, Niklas"},{"full_name":"Li, Yangge","first_name":"Yangge","last_name":"Li"},{"last_name":"Mitra","full_name":"Mitra, Sayan","first_name":"Sayan"},{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"},{"first_name":"Christian","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling"},{"first_name":"Stefan","full_name":"Schupp, Stefan","last_name":"Schupp"},{"full_name":"Wetzlinger, Mark","first_name":"Mark","last_name":"Wetzlinger"}],"publication_status":"published","publisher":"EasyChair","doi":"10.29007/7dt2","article_processing_charge":"No","abstract":[{"text":"We present the results of the ARCH 2020 friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. In its fourth edition, eight tools have been applied to solve eight different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, C2E2, HyDRA, Hylaa, Hylaa-Continuous, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.","lang":"eng"}],"department":[{"_id":"ToHe"}],"intvolume":"        74","date_published":"2020-09-25T00:00:00Z","page":"16-48","type":"conference","year":"2020","publication":"EPiC Series in Computing","corr_author":"1","title":"ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics","language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","date_created":"2020-09-26T14:49:43Z","status":"public","volume":74,"citation":{"ieee":"M. Althoff <i>et al.</i>, “ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics,” in <i>EPiC Series in Computing</i>, 2020, vol. 74, pp. 16–48.","apa":"Althoff, M., Bak, S., Bao, Z., Forets, M., Frehse, G., Freire, D., … Wetzlinger, M. (2020). ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. In <i>EPiC Series in Computing</i> (Vol. 74, pp. 16–48). EasyChair. <a href=\"https://doi.org/10.29007/7dt2\">https://doi.org/10.29007/7dt2</a>","chicago":"Althoff, Matthias, Stanley Bak, Zongnan Bao, Marcelo Forets, Goran Frehse, Daniel Freire, Niklas Kochdumper, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Linear Dynamics.” In <i>EPiC Series in Computing</i>, 74:16–48. EasyChair, 2020. <a href=\"https://doi.org/10.29007/7dt2\">https://doi.org/10.29007/7dt2</a>.","ista":"Althoff M, Bak S, Bao Z, Forets M, Frehse G, Freire D, Kochdumper N, Li Y, Mitra S, Ray R, Schilling C, Schupp S, Wetzlinger M. 2020. ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 74, 16–48.","short":"M. Althoff, S. Bak, Z. Bao, M. Forets, G. Frehse, D. Freire, N. Kochdumper, Y. Li, S. Mitra, R. Ray, C. Schilling, S. Schupp, M. Wetzlinger, in:, EPiC Series in Computing, EasyChair, 2020, pp. 16–48.","ama":"Althoff M, Bak S, Bao Z, et al. ARCH-COMP20 Category Report: Continuous and hybrid systems with linear dynamics. In: <i>EPiC Series in Computing</i>. Vol 74. EasyChair; 2020:16-48. doi:<a href=\"https://doi.org/10.29007/7dt2\">10.29007/7dt2</a>","mla":"Althoff, Matthias, et al. “ARCH-COMP20 Category Report: Continuous and Hybrid Systems with Linear Dynamics.” <i>EPiC Series in Computing</i>, vol. 74, EasyChair, 2020, pp. 16–48, doi:<a href=\"https://doi.org/10.29007/7dt2\">10.29007/7dt2</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>.","apa":"Szep, E. (2020). <i>Local adaptation in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. <i>Local Adaptation in Metapopulations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020."},"degree_awarded":"PhD","date_created":"2020-09-28T07:33:38Z","corr_author":"1","title":"Local adaptation in metapopulations","file":[{"success":1,"access_level":"open_access","file_id":"8575","creator":"dernst","checksum":"20e71f015fbbd78fea708893ad634ed0","file_name":"thesis_EnikoSzep_final.pdf","relation":"main_file","file_size":6354833,"content_type":"application/pdf","date_updated":"2020-09-28T07:25:35Z","date_created":"2020-09-28T07:25:35Z"},{"file_size":23020401,"relation":"source_file","file_name":"thesisFiles_EnikoSzep.zip","checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_created":"2020-09-28T07:25:37Z","date_updated":"2020-09-28T07:25:37Z","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"8576","creator":"dernst"}],"language":[{"iso":"eng"}],"type":"dissertation","year":"2020","alternative_title":["ISTA Thesis"],"date_published":"2020-09-20T00:00:00Z","page":"158","OA_place":"publisher","supervisor":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"publication_identifier":{"eissn":["2663-337X"]},"department":[{"_id":"NiBa"}],"doi":"10.15479/AT:ISTA:8574","abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes,  such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"article_processing_charge":"No","day":"20","author":[{"full_name":"Szep, Eniko","first_name":"Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"}],"_id":"8574","publisher":"Institute of Science and Technology Austria","publication_status":"published","ddc":["570"],"month":"09","has_accepted_license":"1","date_updated":"2026-04-08T07:21:44Z","file_date_updated":"2020-09-28T07:25:37Z","oa_version":"Published Version","oa":1},{"intvolume":"        10","article_number":"242","date_published":"2020-09-01T00:00:00Z","department":[{"_id":"LeSa"}],"publication_identifier":{"eissn":["2077-0375"]},"isi":1,"date_created":"2020-09-28T08:59:26Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, et al. Cu homeostasis in bacteria: The ins and outs. <i>Membranes</i>. 2020;10(9). doi:<a href=\"https://doi.org/10.3390/membranes10090242\">10.3390/membranes10090242</a>","mla":"Andrei, Andreea, et al. “Cu Homeostasis in Bacteria: The Ins and Outs.” <i>Membranes</i>, vol. 10, no. 9, 242, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/membranes10090242\">10.3390/membranes10090242</a>.","short":"A. Andrei, Y. Öztürk, B. Khalfaoui-Hassani, J. Rauch, D. Marckmann, P.I. Trasnea, F. Daldal, H.-G. Koch, Membranes 10 (2020).","ista":"Andrei A, Öztürk Y, Khalfaoui-Hassani B, Rauch J, Marckmann D, Trasnea PI, Daldal F, Koch H-G. 2020. Cu homeostasis in bacteria: The ins and outs. Membranes. 10(9), 242.","chicago":"Andrei, Andreea, Yavuz Öztürk, Bahia Khalfaoui-Hassani, Juna Rauch, Dorian Marckmann, Petru Iulian Trasnea, Fevzi Daldal, and Hans-Georg Koch. “Cu Homeostasis in Bacteria: The Ins and Outs.” <i>Membranes</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/membranes10090242\">https://doi.org/10.3390/membranes10090242</a>.","ieee":"A. Andrei <i>et al.</i>, “Cu homeostasis in bacteria: The ins and outs,” <i>Membranes</i>, vol. 10, no. 9. MDPI, 2020.","apa":"Andrei, A., Öztürk, Y., Khalfaoui-Hassani, B., Rauch, J., Marckmann, D., Trasnea, P. I., … Koch, H.-G. (2020). Cu homeostasis in bacteria: The ins and outs. <i>Membranes</i>. MDPI. <a href=\"https://doi.org/10.3390/membranes10090242\">https://doi.org/10.3390/membranes10090242</a>"},"volume":10,"status":"public","issue":"9","type":"journal_article","year":"2020","language":[{"iso":"eng"}],"file":[{"file_name":"2020_Membranes_Andrei.pdf","checksum":"ceb43d7554e712dea6f36f9287271737","file_size":4612258,"relation":"main_file","content_type":"application/pdf","date_created":"2020-09-28T11:36:50Z","date_updated":"2020-09-28T11:36:50Z","success":1,"access_level":"open_access","file_id":"8583","creator":"dernst"}],"title":"Cu homeostasis in bacteria: The ins and outs","publication":"Membranes","date_updated":"2026-04-02T14:29:28Z","has_accepted_license":"1","month":"09","article_type":"original","oa":1,"oa_version":"Published Version","file_date_updated":"2020-09-28T11:36:50Z","publication_status":"published","_id":"8579","publisher":"MDPI","external_id":{"isi":["000581446000001"]},"author":[{"first_name":"Andreea","full_name":"Andrei, Andreea","last_name":"Andrei"},{"first_name":"Yavuz","full_name":"Öztürk, Yavuz","last_name":"Öztürk"},{"last_name":"Khalfaoui-Hassani","first_name":"Bahia","full_name":"Khalfaoui-Hassani, Bahia"},{"full_name":"Rauch, Juna","first_name":"Juna","last_name":"Rauch"},{"first_name":"Dorian","full_name":"Marckmann, Dorian","last_name":"Marckmann"},{"id":"D560034C-10C4-11EA-ABF4-A4B43DDC885E","last_name":"Trasnea","first_name":"Petru Iulian","full_name":"Trasnea, Petru Iulian"},{"first_name":"Fevzi","full_name":"Daldal, Fevzi","last_name":"Daldal"},{"last_name":"Koch","full_name":"Koch, Hans-Georg","first_name":"Hans-Georg"}],"day":"01","abstract":[{"lang":"eng","text":"Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells."}],"article_processing_charge":"No","doi":"10.3390/membranes10090242","ddc":["570"]},{"article_number":"9158054","date_published":"2020-08-01T00:00:00Z","date_updated":"2023-08-22T09:33:34Z","month":"08","oa_version":"None","publication_identifier":{"isbn":["9781728157511"]},"department":[{"_id":"HeEd"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Graff, Grzegorz, Beata Graff, Grzegorz Jablonski, and Krzysztof Narkiewicz. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” In <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">https://doi.org/10.1109/ESGCO49734.2020.9158054</a>.","ieee":"G. Graff, B. Graff, G. Jablonski, and K. Narkiewicz, “The application of persistent homology in the analysis of heart rate variability,” in <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>, Pisa, Italy, 2020.","apa":"Graff, G., Graff, B., Jablonski, G., &#38; Narkiewicz, K. (2020). The application of persistent homology in the analysis of heart rate variability. In <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>. Pisa, Italy: IEEE. <a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">https://doi.org/10.1109/ESGCO49734.2020.9158054</a>","ama":"Graff G, Graff B, Jablonski G, Narkiewicz K. The application of persistent homology in the analysis of heart rate variability. In: <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">10.1109/ESGCO49734.2020.9158054</a>","mla":"Graff, Grzegorz, et al. “The Application of Persistent Homology in the Analysis of Heart Rate Variability.” <i>11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, </i>, 9158054, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/ESGCO49734.2020.9158054\">10.1109/ESGCO49734.2020.9158054</a>.","ista":"Graff G, Graff B, Jablonski G, Narkiewicz K. 2020. The application of persistent homology in the analysis of heart rate variability. 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, . ESGCO: European Study Group on Cardiovascular Oscillations, 9158054.","short":"G. Graff, B. Graff, G. Jablonski, K. Narkiewicz, in:, 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, , IEEE, 2020."},"abstract":[{"lang":"eng","text":"We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients."}],"article_processing_charge":"No","doi":"10.1109/ESGCO49734.2020.9158054","status":"public","_id":"8580","publisher":"IEEE","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"first_name":"Beata","full_name":"Graff, Beata","last_name":"Graff"},{"full_name":"Jablonski, Grzegorz","orcid":"0000-0002-3536-9866","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski"},{"first_name":"Krzysztof","full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz"}],"date_created":"2020-09-28T08:59:27Z","publication_status":"published","external_id":{"isi":["000621172600045"]},"day":"01","conference":{"end_date":"2020-07-15","name":"ESGCO: European Study Group on Cardiovascular Oscillations","start_date":"2020-07-15","location":"Pisa, Italy"},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"title":"The application of persistent homology in the analysis of heart rate variability","publication":"11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities, ","type":"conference","year":"2020"},{"page":"1077-1085","date_published":"2020-11-01T00:00:00Z","intvolume":"        27","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"ScienComp"}],"department":[{"_id":"LeSa"}],"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"isi":1,"citation":{"mla":"Pinke, Gergely, et al. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” <i>Nature Structural and Molecular Biology</i>, vol. 27, no. 11, Springer Nature, 2020, pp. 1077–85, doi:<a href=\"https://doi.org/10.1038/s41594-020-0503-8\">10.1038/s41594-020-0503-8</a>.","ama":"Pinke G, Zhou L, Sazanov LA. Cryo-EM structure of the entire mammalian F-type ATP synthase. <i>Nature Structural and Molecular Biology</i>. 2020;27(11):1077-1085. doi:<a href=\"https://doi.org/10.1038/s41594-020-0503-8\">10.1038/s41594-020-0503-8</a>","ista":"Pinke G, Zhou L, Sazanov LA. 2020. Cryo-EM structure of the entire mammalian F-type ATP synthase. Nature Structural and Molecular Biology. 27(11), 1077–1085.","short":"G. Pinke, L. Zhou, L.A. Sazanov, Nature Structural and Molecular Biology 27 (2020) 1077–1085.","chicago":"Pinke, Gergely, Long Zhou, and Leonid A Sazanov. “Cryo-EM Structure of the Entire Mammalian F-Type ATP Synthase.” <i>Nature Structural and Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41594-020-0503-8\">https://doi.org/10.1038/s41594-020-0503-8</a>.","apa":"Pinke, G., Zhou, L., &#38; Sazanov, L. A. (2020). Cryo-EM structure of the entire mammalian F-type ATP synthase. <i>Nature Structural and Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-020-0503-8\">https://doi.org/10.1038/s41594-020-0503-8</a>","ieee":"G. Pinke, L. Zhou, and L. A. Sazanov, “Cryo-EM structure of the entire mammalian F-type ATP synthase,” <i>Nature Structural and Molecular Biology</i>, vol. 27, no. 11. Springer Nature, pp. 1077–1085, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":27,"status":"public","date_created":"2020-09-28T08:59:27Z","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-atpase-solved/","description":"News on IST Homepage"}]},"quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"title":"Cryo-EM structure of the entire mammalian F-type ATP synthase","publication":"Nature Structural and Molecular Biology","issue":"11","year":"2020","type":"journal_article","pmid":1,"acknowledgement":"We thank J. Novacek from CEITEC (Brno, Czech Republic) for assistance with collecting the FEI Krios dataset and iNEXT for providing access to CEITEC. We thank the IST Austria EM facility for access and assistance with collecting the FEI Glacios dataset. Data processing was performed at the IST high-performance computing cluster. This work has been supported by iNEXT EM HEDC (proposal 4506), funded by the Horizon 2020 Programme of the European Commission.","date_updated":"2025-07-10T11:57:09Z","month":"11","oa_version":"None","article_type":"original","article_processing_charge":"No","abstract":[{"text":"The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.","lang":"eng"}],"doi":"10.1038/s41594-020-0503-8","external_id":{"pmid":["32929284"],"isi":["000569299400004"]},"_id":"8581","publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Gergely","full_name":"Pinke, Gergely","id":"4D5303E6-F248-11E8-B48F-1D18A9856A87","last_name":"Pinke"},{"full_name":"Zhou, Long","orcid":"0000-0002-1864-8951","first_name":"Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"day":"01"},{"title":"Intermolecular forces and correlations mediated by a phonon bath","corr_author":"1","publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"pmid":1,"year":"2020","type":"journal_article","issue":"16","volume":152,"status":"public","citation":{"ieee":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, and A. Deuchert, “Intermolecular forces and correlations mediated by a phonon bath,” <i>The Journal of Chemical Physics</i>, vol. 152, no. 16. AIP Publishing, 2020.","apa":"Li, X., Yakaboylu, E., Bighin, G., Schmidt, R., Lemeshko, M., &#38; Deuchert, A. (2020). Intermolecular forces and correlations mediated by a phonon bath. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5144759\">https://doi.org/10.1063/1.5144759</a>","chicago":"Li, Xiang, Enderalp Yakaboylu, Giacomo Bighin, Richard Schmidt, Mikhail Lemeshko, and Andreas Deuchert. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5144759\">https://doi.org/10.1063/1.5144759</a>.","short":"X. Li, E. Yakaboylu, G. Bighin, R. Schmidt, M. Lemeshko, A. Deuchert, The Journal of Chemical Physics 152 (2020).","ista":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. 2020. Intermolecular forces and correlations mediated by a phonon bath. The Journal of Chemical Physics. 152(16), 164302.","ama":"Li X, Yakaboylu E, Bighin G, Schmidt R, Lemeshko M, Deuchert A. Intermolecular forces and correlations mediated by a phonon bath. <i>The Journal of Chemical Physics</i>. 2020;152(16). doi:<a href=\"https://doi.org/10.1063/1.5144759\">10.1063/1.5144759</a>","mla":"Li, Xiang, et al. “Intermolecular Forces and Correlations Mediated by a Phonon Bath.” <i>The Journal of Chemical Physics</i>, vol. 152, no. 16, 164302, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5144759\">10.1063/1.5144759</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"8958","relation":"dissertation_contains"}]},"quality_controlled":"1","date_created":"2020-09-30T10:33:17Z","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"department":[{"_id":"MiLe"},{"_id":"RoSe"}],"isi":1,"date_published":"2020-04-27T00:00:00Z","article_number":"164302","arxiv":1,"intvolume":"       152","ec_funded":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the effective interaction and the resulting correlations between two diatomic molecules immersed in a bath of bosons. By analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system in different parameter regimes and apply several theoretical approaches to describe its properties. Using a Born–Oppenheimer approximation, we investigate the dependence of the effective intermolecular interaction on the rotational state of the two molecules. In the strong-coupling regime, a product-state ansatz shows that the molecules tend to have a strong alignment in the ground state. To investigate the system in the weak-coupling regime, we apply a one-phonon excitation variational ansatz, which allows us to access the energy spectrum. In comparison to the angulon quasiparticle, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. These features are proposed as an experimentally observable signature for the formation of the biangulon quasiparticle. Finally, by using products of single angulon and bare impurity wave functions as basis states, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"doi":"10.1063/1.5144759","day":"27","project":[{"grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770"},{"call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"author":[{"last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Xiang","first_name":"Xiang"},{"first_name":"Enderalp","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu"},{"last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"last_name":"Schmidt","first_name":"Richard","full_name":"Schmidt, Richard"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"Andreas","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert"}],"_id":"8587","publisher":"AIP Publishing","publication_status":"published","external_id":{"pmid":["32357791"],"isi":["000530448300001"],"arxiv":["1912.02658"]},"oa_version":"Preprint","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"article_type":"original","oa":1,"acknowledgement":"We are grateful to Areg Ghazaryan for valuable discussions. M.L. acknowledges support from the Austrian Science Fund (FWF) under Project No. P29902-N27 and from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). G.B. acknowledges support from the Austrian Science Fund (FWF) under Project No. M2461-N27. A.D. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the European Research Council (ERC) Grant Agreement No. 694227 and under the Marie Sklodowska-Curie Grant Agreement No. 836146. R.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2111 – 390814868.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.02658"}],"month":"04","date_updated":"2026-04-08T07:26:09Z"},{"citation":{"ista":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. 2020. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. Physical Review B. 102(4), 045307.","short":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, P.V. Santos, Physical Review B 102 (2020).","mla":"Hubert, C., et al. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” <i>Physical Review B</i>, vol. 102, no. 4, 045307, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.045307\">10.1103/physrevb.102.045307</a>.","ama":"Hubert C, Cohen K, Ghazaryan A, Lemeshko M, Rapaport R, Santos PV. Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. <i>Physical Review B</i>. 2020;102(4). doi:<a href=\"https://doi.org/10.1103/physrevb.102.045307\">10.1103/physrevb.102.045307</a>","apa":"Hubert, C., Cohen, K., Ghazaryan, A., Lemeshko, M., Rapaport, R., &#38; Santos, P. V. (2020). Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.045307\">https://doi.org/10.1103/physrevb.102.045307</a>","ieee":"C. Hubert, K. Cohen, A. Ghazaryan, M. Lemeshko, R. Rapaport, and P. V. Santos, “Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids,” <i>Physical Review B</i>, vol. 102, no. 4. American Physical Society, 2020.","chicago":"Hubert, C., K. Cohen, Areg Ghazaryan, Mikhail Lemeshko, R. Rapaport, and P. V. Santos. “Attractive Interactions, Molecular Complexes, and Polarons in Coupled Dipolar Exciton Fluids.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.045307\">https://doi.org/10.1103/physrevb.102.045307</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","volume":102,"date_created":"2020-09-30T10:33:43Z","quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Physical Review B","title":"Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids","year":"2020","issue":"4","type":"journal_article","arxiv":1,"article_number":"045307","date_published":"2020-07-21T00:00:00Z","intvolume":"       102","isi":1,"department":[{"_id":"MiLe"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"doi":"10.1103/physrevb.102.045307","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum well (DQW) subjected to an electric field are neutral species with a dipole moment oriented perpendicular to the DQW plane. Here, we theoretically study interactions between IXs in stacked DQW bilayers, where the dipolar coupling can be either attractive or repulsive depending on the relative positions of the particles. By using microscopic band structure calculations to determine the electronic states forming the excitons, we show that the attractive dipolar interaction between stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW interaction energy and making the IX even more electrically polarizable. Many-particle interaction effects are addressed by considering the coupling between a single IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either as a closed-packed lattice or as a continuum IX fluid. We find that the lattice model yields IX interlayer binding energies decreasing with increasing lattice density. This behavior is due to the dominating role of the intra-DQW dipolar repulsion, which prevents more than one exciton from entering the attractive region of the inter-DQW coupling. Finally, both models shows that the single IX distorts the distribution of IXs in the adjacent DQW, thus inducing the formation of an IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous dependence on density in semiquantitative agreement with a recent experimental study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)]."}],"external_id":{"arxiv":["1910.06015"],"isi":["000550579100004"]},"_id":"8588","publication_status":"published","author":[{"first_name":"C.","full_name":"Hubert, C.","last_name":"Hubert"},{"last_name":"Cohen","first_name":"K.","full_name":"Cohen, K."},{"last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"last_name":"Rapaport","full_name":"Rapaport, R.","first_name":"R."},{"full_name":"Santos, P. V.","first_name":"P. V.","last_name":"Santos"}],"publisher":"American Physical Society","project":[{"call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"day":"21","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1910.06015","open_access":"1"}],"acknowledgement":"We thank W. Kaganer for discussions and for comment on the manuscript. We acknowledge the financial support from the German-Israeli Foundation (GIF), grant agreement I-1277-303.10/2014. M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A.G. acknowledges support by the European Unions Horizon 2020 research and innovation\r\nprogram under the Marie Skodowska-Curie grant agreement No 754411. P.V.S acknowledges financial support\r\nfrom the Deutsche Forschungsgemeinschaft (DFG) under\r\nProject No. SA 598/12-1.","date_updated":"2025-04-14T07:43:49Z","month":"07","oa_version":"Preprint","article_type":"original","oa":1},{"page":"164","alternative_title":["ISTA Thesis"],"date_published":"2020-09-30T00:00:00Z","OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"mla":"Han, Huibin. <i>Novel Insights into PIN Polarity Regulation during Arabidopsis Development</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8589\">10.15479/AT:ISTA:8589</a>.","ama":"Han H. Novel insights into PIN polarity regulation during Arabidopsis development. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8589\">10.15479/AT:ISTA:8589</a>","short":"H. Han, Novel Insights into PIN Polarity Regulation during Arabidopsis Development, Institute of Science and Technology Austria, 2020.","ista":"Han H. 2020. Novel insights into PIN polarity regulation during Arabidopsis development. Institute of Science and Technology Austria.","chicago":"Han, Huibin. “Novel Insights into PIN Polarity Regulation during Arabidopsis Development.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8589\">https://doi.org/10.15479/AT:ISTA:8589</a>.","apa":"Han, H. (2020). <i>Novel insights into PIN polarity regulation during Arabidopsis development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8589\">https://doi.org/10.15479/AT:ISTA:8589</a>","ieee":"H. Han, “Novel insights into PIN polarity regulation during Arabidopsis development,” Institute of Science and Technology Austria, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_created":"2020-09-30T14:50:51Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7643"}]},"degree_awarded":"PhD","file":[{"date_created":"2020-09-30T14:50:20Z","date_updated":"2020-09-30T14:50:20Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":49198118,"file_name":"2020_Han_Thesis.docx","checksum":"c4bda1947d4c09c428ac9ce667b02327","creator":"dernst","file_id":"8590","access_level":"closed"},{"content_type":"application/pdf","date_updated":"2021-10-01T13:33:02Z","date_created":"2020-09-30T14:49:59Z","checksum":"3f4f5d1718c2230adf30639ecaf8a00b","file_name":"2020_Han_Thesis.pdf","file_size":15513963,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"8591"}],"language":[{"iso":"eng"}],"corr_author":"1","title":"Novel insights into PIN polarity regulation during Arabidopsis development","type":"dissertation","year":"2020","acknowledgement":"I also want to thank the China Scholarship Council for supporting my study during the year from 2015 to 2019. I also want to thank IST facilities – the Bioimaging facility, the media kitchen, the plant facility and all of the campus services, for their support.","has_accepted_license":"1","date_updated":"2026-06-18T19:25:52Z","month":"09","file_date_updated":"2021-10-01T13:33:02Z","oa_version":"Published Version","oa":1,"doi":"10.15479/AT:ISTA:8589","article_processing_charge":"No","abstract":[{"text":"The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","_id":"8589","publication_status":"published","author":[{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","full_name":"Han, Huibin","first_name":"Huibin"}],"day":"30","ddc":["580"]}]