[{"isi":1,"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","doi":"10.1145/3453483.3454102","publisher":"Association for Computing Machinery","conference":{"name":"PLDI: Programming Language Design and Implementation","location":"Online","start_date":"2021-06-20","end_date":"2021-06-26"},"date_published":"2021-06-01T00:00:00Z","_id":"9646","quality_controlled":"1","day":"01","department":[{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Quantitative analysis of assertion violations in probabilistic programs","oa":1,"article_processing_charge":"No","publication_identifier":{"isbn":["9781450383912"]},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"date_updated":"2025-04-15T07:55:05Z","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1171–86. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1171–86, doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1171–1186.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1171-1186. doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1171–1186). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.14617"}],"type":"conference","date_created":"2021-07-11T22:01:18Z","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","oa_version":"Preprint","scopus_import":"1","external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"status":"public","abstract":[{"text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.","lang":"eng"}],"month":"06","year":"2021","publication_status":"published","page":"1171-1186","author":[{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"full_name":"Sun, Yican","last_name":"Sun","first_name":"Yican"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady"}]},{"has_accepted_license":"1","external_id":{"isi":["000710180500002"]},"status":"public","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"type":"journal_article","corr_author":"1","scopus_import":"1","date_created":"2021-07-11T22:01:18Z","oa_version":"Published Version","publication":"Theoretical Computer Science","language":[{"iso":"eng"}],"citation":{"chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>.","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>, vol. 893, Elsevier, 2021, pp. 1–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., &#38; Guet, C. C. (2021). Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” <i>Theoretical Computer Science</i>, vol. 893. Elsevier, pp. 1–16, 2021.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. 2021;893:1-16. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16."},"article_type":"original","ddc":["004"],"date_updated":"2025-04-15T06:25:56Z","intvolume":"       893","project":[{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"author":[{"full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov"},{"full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","first_name":"Claudia"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"page":"1-16","publication_status":"published","file_date_updated":"2022-05-12T12:13:27Z","year":"2021","month":"06","volume":893,"_id":"9647","date_published":"2021-06-04T00:00:00Z","quality_controlled":"1","publisher":"Elsevier","isi":1,"doi":"10.1016/j.tcs.2021.05.023","file":[{"success":1,"checksum":"d3aef34cfb13e53bba4cf44d01680793","file_id":"11364","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_updated":"2022-05-12T12:13:27Z","file_size":2566504,"date_created":"2022-05-12T12:13:27Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access"}],"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["0304-3975"]},"article_processing_charge":"No","title":"Long lived transients in gene regulation","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"day":"04"},{"department":[{"_id":"JiFr"}],"day":"01","oa":1,"title":"PIN-mediated polar auxin transport regulations in plant tropic responses","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","publisher":"Wiley","doi":"10.1111/nph.17617","acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","file":[{"content_type":"application/pdf","date_created":"2021-10-07T13:42:47Z","relation":"main_file","creator":"kschuh","access_level":"open_access","checksum":"6422a6eb329b52d96279daaee0fcf189","success":1,"date_updated":"2021-10-07T13:42:47Z","file_id":"10105","file_name":"2021_NewPhytologist_Han.pdf","file_size":1939800}],"isi":1,"_id":"9656","date_published":"2021-10-01T00:00:00Z","quality_controlled":"1","month":"10","issue":"2","volume":232,"file_date_updated":"2021-10-07T13:42:47Z","publication_status":"published","year":"2021","page":"510-522","pmid":1,"author":[{"first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski"},{"orcid":"0000-0001-5187-8401","first_name":"Linlin","last_name":"Qi","full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"full_name":"Alotaibi, SS","first_name":"SS","last_name":"Alotaibi"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"date_updated":"2025-04-14T07:45:00Z","ddc":["580"],"intvolume":"       232","article_type":"original","ec_funded":1,"citation":{"chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment."}],"has_accepted_license":"1","external_id":{"pmid":["34254313"],"isi":["000680587100001"]},"status":"public","date_created":"2021-07-14T15:29:14Z","publication":"New Phytologist","oa_version":"Published Version","scopus_import":"1","corr_author":"1","type":"journal_article"},{"year":"2021","file_date_updated":"2021-07-19T12:13:34Z","publication_status":"published","issue":"9","volume":33,"month":"07","author":[{"full_name":"Gao, Z","last_name":"Gao","first_name":"Z"},{"full_name":"Chen, Z","last_name":"Chen","first_name":"Z"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"first_name":"H","last_name":"Xu","full_name":"Xu, H"},{"last_name":"Xu","first_name":"Q","full_name":"Xu, Q"},{"last_name":"Chen","first_name":"J","full_name":"Chen, J"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Huang","first_name":"L","full_name":"Huang, L"},{"full_name":"Zhao, H","first_name":"H","last_name":"Zhao"},{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"first_name":"S","last_name":"Mai","full_name":"Mai, S"},{"full_name":"Xu, T","first_name":"T","last_name":"Xu"},{"full_name":"Liu, X","first_name":"X","last_name":"Liu"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Guan, Y","last_name":"Guan","first_name":"Y"},{"last_name":"Yang","first_name":"W","full_name":"Yang, W"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Petrášek","first_name":"J","full_name":"Petrášek, J"},{"last_name":"Zhang","first_name":"J","full_name":"Zhang, J"},{"last_name":"Chen","first_name":"X","full_name":"Chen, X"}],"pmid":1,"page":"2981–3003","intvolume":"        33","date_updated":"2024-10-21T06:02:03Z","ddc":["580"],"oa_version":"Published Version","scopus_import":"1","publication":"Plant Cell","date_created":"2021-07-14T15:32:43Z","type":"journal_article","abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"status":"public","has_accepted_license":"1","external_id":{"pmid":["34240197"],"isi":["000702165300012"]},"article_type":"original","citation":{"chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003."},"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","day":"07","department":[{"_id":"JiFr"}],"article_processing_charge":"No","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.1093/plcell/koab183","isi":1,"file":[{"file_size":10566921,"success":1,"checksum":"6715712ec306c321f0204c817b7f8ae7","file_name":"2021_PlantCell_Gao.pdf","file_id":"9691","date_updated":"2021-07-19T12:13:34Z","creator":"cziletti","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_created":"2021-07-19T12:13:34Z"}],"publisher":"American Society of Plant Biologists","date_published":"2021-07-07T00:00:00Z","_id":"9657","quality_controlled":"1"},{"intvolume":"        23","date_updated":"2026-04-02T14:01:49Z","arxiv":1,"ddc":["530"],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"New Journal of Physics","date_created":"2021-07-18T22:01:22Z","scopus_import":"1","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment."}],"has_accepted_license":"1","external_id":{"isi":["000664736300001"],"arxiv":["2102.04961"]},"status":"public","article_type":"original","ec_funded":1,"citation":{"apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>","mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>."},"language":[{"iso":"eng"}],"year":"2021","publication_status":"published","file_date_updated":"2021-07-19T11:47:16Z","issue":"6","volume":23,"month":"06","author":[{"full_name":"Huber, David","first_name":"David","last_name":"Huber"},{"first_name":"Oleksandr V.","last_name":"Marchukov","full_name":"Marchukov, Oleksandr V."},{"full_name":"Hammer, Hans Werner","last_name":"Hammer","first_name":"Hans Werner"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"file":[{"content_type":"application/pdf","date_created":"2021-07-19T11:47:16Z","access_level":"open_access","creator":"cziletti","relation":"main_file","file_id":"9690","file_name":"2021_NewJPhys_Huber.pdf","date_updated":"2021-07-19T11:47:16Z","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","success":1,"file_size":3868445}],"isi":1,"doi":"10.1088/1367-2630/ac0576","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","publisher":"IOP Publishing","date_published":"2021-06-23T00:00:00Z","_id":"9679","quality_controlled":"1","article_number":"065009","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"title":"Morphology of three-body quantum states from machine learning","day":"23","department":[{"_id":"MiLe"}],"article_processing_charge":"Yes","publication_identifier":{"eissn":["1367-2630"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"article_number":"e68876","_id":"9746","date_published":"2021-07-28T00:00:00Z","quality_controlled":"1","publisher":"eLife Sciences Publications","doi":"10.7554/elife.68876","isi":1,"acknowledgement":"We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel).","publication_identifier":{"eissn":["2050-084X"]},"article_processing_charge":"No","title":"High potency of sequential therapy with only beta-lactam antibiotics","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"}],"day":"28","external_id":{"isi":["000692027800001"],"pmid":["34318749"]},"status":"public","abstract":[{"lang":"eng","text":"Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs."}],"main_file_link":[{"url":"https://doi.org/10.7554/eLife.68876","open_access":"1"}],"type":"journal_article","publication":"eLife","oa_version":"Published Version","date_created":"2021-07-28T13:36:57Z","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","citation":{"short":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021).","mla":"Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>, vol. 10, e68876, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>.","ama":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.68876\">10.7554/elife.68876</a>","ieee":"A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876.","apa":"Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., &#38; Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>","chicago":"Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.68876\">https://doi.org/10.7554/elife.68876</a>."},"ddc":["570"],"date_updated":"2026-06-18T19:56:55Z","intvolume":"        10","author":[{"full_name":"Batra, Aditi","first_name":"Aditi","last_name":"Batra"},{"orcid":"0000-0001-9480-5261","first_name":"Roderich","last_name":"Römhild","full_name":"Römhild, Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E"},{"first_name":"Emilie","last_name":"Rousseau","full_name":"Rousseau, Emilie"},{"full_name":"Franzenburg, Sören","last_name":"Franzenburg","first_name":"Sören"},{"last_name":"Niemann","first_name":"Stefan","full_name":"Niemann, Stefan"},{"full_name":"Schulenburg, Hinrich","first_name":"Hinrich","last_name":"Schulenburg"}],"pmid":1,"publication_status":"published","year":"2021","month":"07","volume":10},{"publisher":"Public Library of Science","isi":1,"acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program.","doi":"10.1371/journal.pcbi.1009124","file":[{"checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","date_updated":"2021-08-05T12:06:49Z","file_id":"9771","file_name":"2021_PlosCompBio_Bartlett.pdf","file_size":693633,"date_created":"2021-08-05T12:06:49Z","content_type":"application/pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access"}],"article_number":"e1009124","_id":"9759","date_published":"2021-07-15T00:00:00Z","department":[{"_id":"CaHe"}],"day":"15","oa":1,"title":"Ten simple rules to improve academic work- life balance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","date_updated":"2025-07-10T12:02:02Z","ddc":["613"],"intvolume":"        17","article_type":"letter_note","citation":{"chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>.","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021).","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>.","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” <i>PLoS Computational Biology</i>, vol. 17, no. 7. Public Library of Science, 2021.","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. 2021;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., &#38; Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>"},"language":[{"iso":"eng"}],"status":"public","external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"has_accepted_license":"1","oa_version":"Published Version","date_created":"2021-08-01T22:01:21Z","scopus_import":"1","publication":"PLoS Computational Biology","type":"journal_article","month":"07","issue":"7","volume":17,"file_date_updated":"2021-08-05T12:06:49Z","publication_status":"published","year":"2021","pmid":1,"author":[{"first_name":"Michael John","last_name":"Bartlett","full_name":"Bartlett, Michael John"},{"last_name":"Arslan","first_name":"Feyza N","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","full_name":"Arslan, Feyza N"},{"last_name":"Bankston","first_name":"Adriana","full_name":"Bankston, Adriana"},{"first_name":"Sarvenaz","last_name":"Sarabipour","full_name":"Sarabipour, Sarvenaz"}]},{"department":[{"_id":"SaSi"}],"day":"25","oa":1,"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["2073-4409"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","publisher":"MDPI","isi":1,"file":[{"success":1,"checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","date_updated":"2021-08-04T14:01:30Z","file_name":"2021_Cells_Muench.pdf","file_id":"9768","file_size":4555611,"date_created":"2021-08-04T14:01:30Z","content_type":"application/pdf","relation":"main_file","creator":"cziletti","access_level":"open_access"}],"acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","doi":"10.3390/cells10071593","article_number":"1593","_id":"9761","date_published":"2021-06-25T00:00:00Z","quality_controlled":"1","month":"06","issue":"7","volume":10,"file_date_updated":"2021-08-04T14:01:30Z","publication_status":"published","year":"2021","pmid":1,"author":[{"full_name":"Muench, Nicole A.","first_name":"Nicole A.","last_name":"Muench"},{"first_name":"Sonia","last_name":"Patel","full_name":"Patel, Sonia"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes"},{"full_name":"Donahue, Ryan J.","first_name":"Ryan J.","last_name":"Donahue"},{"first_name":"Akihiro","last_name":"Ikeda","full_name":"Ikeda, Akihiro"},{"first_name":"Robert W.","last_name":"Nickells","full_name":"Nickells, Robert W."}],"date_updated":"2026-04-02T13:56:24Z","ddc":["570"],"intvolume":"        10","citation":{"chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>.","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” <i>Cells</i>, vol. 10, no. 7. MDPI, 2021.","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. 2021;10(7). doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., &#38; Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>, vol. 10, no. 7, 1593, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>."},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. "}],"external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"has_accepted_license":"1","status":"public","publication":"Cells","date_created":"2021-08-01T22:01:22Z","oa_version":"Published Version","scopus_import":"1","type":"journal_article"},{"type":"journal_article","oa_version":"Published Version","scopus_import":"1","date_created":"2021-08-04T15:00:55Z","publication":"SciPost Physics","external_id":{"isi":["000680039500013"],"arxiv":["2101.10958"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}],"language":[{"iso":"eng"}],"ec_funded":1,"article_type":"original","citation":{"apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., &#38; Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” <i>SciPost Physics</i>, vol. 11, no. 1. SciPost Foundation, 2021.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>, vol. 11, no. 1, 008, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>.","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021).","chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>."},"intvolume":"        11","arxiv":1,"ddc":["530"],"date_updated":"2025-05-14T10:51:56Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"author":[{"last_name":"Brauneis","first_name":"Fabian","full_name":"Brauneis, Fabian"},{"last_name":"Hammer","first_name":"Hans-Werner","full_name":"Hammer, Hans-Werner"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"year":"2021","file_date_updated":"2021-08-10T11:44:59Z","publication_status":"published","volume":11,"issue":"1","month":"07","quality_controlled":"1","_id":"9769","date_published":"2021-07-13T00:00:00Z","article_number":"008","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","file":[{"checksum":"eaa847346b1a023d97bbb291779610ed","success":1,"date_updated":"2021-08-10T11:44:59Z","file_id":"9875","file_name":"2021_SciPostPhysics_Brauneis.pdf","file_size":1085300,"date_created":"2021-08-10T11:44:59Z","content_type":"application/pdf","relation":"main_file","creator":"asandaue","access_level":"open_access"}],"doi":"10.21468/scipostphys.11.1.008","isi":1,"publisher":"SciPost Foundation","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2542-4653"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","oa":1,"day":"13","department":[{"_id":"MiLe"}]},{"arxiv":1,"date_updated":"2025-04-14T07:43:49Z","intvolume":"       104","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"}],"external_id":{"isi":["000678780800003"],"arxiv":["2101.05173"]},"status":"public","abstract":[{"text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.05173"}],"type":"journal_article","date_created":"2021-08-04T15:05:32Z","scopus_import":"1","publication":"Physical Review B","oa_version":"Preprint","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>.","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>.","short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., &#38; Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430.","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” <i>Physical Review B</i>, vol. 104, no. 2. American Physical Society, 2021.","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. 2021;104(2). doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>"},"article_type":"original","publication_status":"published","year":"2021","month":"07","volume":104,"issue":"2","author":[{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","first_name":"Artem"},{"first_name":"Hen","last_name":"Alpern","full_name":"Alpern, Hen"},{"first_name":"Yossi","last_name":"Paltiel","full_name":"Paltiel, Yossi"},{"full_name":"Millo, Oded","first_name":"Oded","last_name":"Millo"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg"}],"publisher":"American Physical Society","doi":"10.1103/physrevb.104.024430","acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","isi":1,"article_number":"024430","quality_controlled":"1","_id":"9770","date_published":"2021-07-01T00:00:00Z","title":"Interplay between friction and spin-orbit coupling as a source of spin polarization","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"day":"01","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_processing_charge":"No"},{"month":"05","related_material":{"link":[{"url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/","description":"News on IST Homepage","relation":"press_release"}]},"issue":"1","volume":12,"publication_status":"published","file_date_updated":"2021-12-17T11:34:50Z","year":"2021","pmid":1,"acknowledged_ssus":[{"_id":"SSU"}],"author":[{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael"},{"full_name":"Okamoto, Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","first_name":"Yuji","last_name":"Okamoto"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"project":[{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"}],"OA_type":"gold","date_updated":"2025-06-12T06:28:45Z","ddc":["570"],"intvolume":"        12","OA_place":"publisher","citation":{"mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912.","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>."},"article_type":"original","ec_funded":1,"language":[{"iso":"eng"}],"abstract":[{"text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses.","lang":"eng"}],"has_accepted_license":"1","external_id":{"pmid":["34006874"],"isi":["000655481800014"]},"status":"public","scopus_import":"1","publication":"Nature Communications","date_created":"2021-08-06T07:22:55Z","oa_version":"Published Version","corr_author":"1","type":"journal_article","department":[{"_id":"PeJo"}],"day":"18","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"oa":1,"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","publisher":"Springer","doi":"10.1038/s41467-021-23153-5","isi":1,"acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","file":[{"relation":"main_file","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-17T11:34:50Z","file_size":3108845,"success":1,"checksum":"6036a8cdae95e1707c2a04d54e325ff4","date_updated":"2021-12-17T11:34:50Z","file_id":"10563","file_name":"2021_NatureCommunications_Vandael.pdf"}],"article_number":"2912","_id":"9778","date_published":"2021-05-18T00:00:00Z","quality_controlled":"1"},{"date_published":"2021-02-01T00:00:00Z","_id":"9787","article_number":"2101.12566","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.1.\r\n","doi":"10.48550/arXiv.2101.12566","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","oa":1,"day":"01","department":[{"_id":"RoSe"}],"main_file_link":[{"url":"https://arxiv.org/abs/2101.12566","open_access":"1"}],"corr_author":"1","type":"preprint","oa_version":"Preprint","date_created":"2021-08-06T08:25:57Z","publication":"arXiv","has_accepted_license":"1","external_id":{"arxiv":["2101.12566"]},"status":"public","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"language":[{"iso":"eng"}],"ec_funded":1,"citation":{"short":"D. Feliciangeli, R. Seiringer, ArXiv (n.d.).","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>ArXiv</i>, 2101.12566, doi:<a href=\"https://doi.org/10.48550/arXiv.2101.12566\">10.48550/arXiv.2101.12566</a>.","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” <i>arXiv</i>. .","ista":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. arXiv, 2101.12566.","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2101.12566\">10.48550/arXiv.2101.12566</a>","apa":"Feliciangeli, D., &#38; Seiringer, R. (n.d.). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2101.12566\">https://doi.org/10.48550/arXiv.2101.12566</a>","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2101.12566\">https://doi.org/10.48550/arXiv.2101.12566</a>."},"ddc":["510"],"arxiv":1,"date_updated":"2026-04-08T06:59:49Z","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"author":[{"orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"year":"2021","publication_status":"draft","related_material":{"record":[{"relation":"later_version","id":"10224","status":"public"},{"relation":"dissertation_contains","status":"public","id":"9733"}]},"month":"02"},{"acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","doi":"10.48550/arXiv.2107.03720","article_number":"2107.03720 ","date_published":"2021-07-08T00:00:00Z","_id":"9791","oa":1,"title":"The effective mass problem for the Landau-Pekar equations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"day":"08","article_processing_charge":"No","date_updated":"2026-04-08T06:59:49Z","ddc":["510"],"arxiv":1,"OA_place":"repository","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"abstract":[{"lang":"eng","text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar."}],"external_id":{"arxiv":["2107.03720"]},"status":"public","date_created":"2021-08-06T08:49:45Z","oa_version":"Preprint","publication":"arXiv","type":"preprint","corr_author":"1","main_file_link":[{"url":"https://arxiv.org/abs/2107.03720","open_access":"1"}],"citation":{"mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>ArXiv</i>, 2107.03720, doi:<a href=\"https://doi.org/10.48550/arXiv.2107.03720\">10.48550/arXiv.2107.03720</a>.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","apa":"Feliciangeli, D., Rademacher, S. A. E., &#38; Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2107.03720\">https://doi.org/10.48550/arXiv.2107.03720</a>","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2107.03720\">10.48550/arXiv.2107.03720</a>","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” <i>arXiv</i>. .","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2107.03720\">https://doi.org/10.48550/arXiv.2107.03720</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"draft","year":"2021","month":"07","related_material":{"record":[{"relation":"later_version","status":"public","id":"10755"},{"relation":"dissertation_contains","id":"9733","status":"public"}]},"author":[{"id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario","first_name":"Dario","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli"},{"last_name":"Rademacher","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","full_name":"Rademacher, Simone Anna Elvira"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert"}]},{"language":[{"iso":"eng"}],"ec_funded":1,"citation":{"chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2106.11217\">https://doi.org/10.48550/arXiv.2106.11217</a>.","apa":"Feliciangeli, D., Gerolin, A., &#38; Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2106.11217\">https://doi.org/10.48550/arXiv.2106.11217</a>","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” <i>arXiv</i>. .","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2106.11217\">10.48550/arXiv.2106.11217</a>","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>ArXiv</i>, 2106.11217, doi:<a href=\"https://doi.org/10.48550/arXiv.2106.11217\">10.48550/arXiv.2106.11217</a>.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.)."},"has_accepted_license":"1","status":"public","external_id":{"arxiv":["2106.11217"]},"abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"type":"preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}],"publication":"arXiv","date_created":"2021-08-06T09:07:12Z","oa_version":"Preprint","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"},{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"ddc":["510"],"arxiv":1,"date_updated":"2026-04-08T07:00:03Z","author":[{"last_name":"Feliciangeli","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"},{"last_name":"Gerolin","first_name":"Augusto","full_name":"Gerolin, Augusto"},{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"}],"month":"07","related_material":{"record":[{"relation":"later_version","id":"12911","status":"public"},{"relation":"dissertation_contains","id":"9733","status":"public"},{"id":"10030","status":"public","relation":"dissertation_contains"}]},"publication_status":"draft","year":"2021","article_number":"2106.11217","_id":"9792","date_published":"2021-07-21T00:00:00Z","doi":"10.48550/arXiv.2106.11217","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article.  L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"day":"21","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":"         6","ddc":["530"],"arxiv":1,"date_updated":"2023-10-17T12:54:54Z","language":[{"iso":"eng"}],"citation":{"ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” <i>Quantum Science and Technology</i>, vol. 6, no. 4. IOP Publishing, 2021.","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. 2021;6(4). doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005.","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., &#38; Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021).","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>.","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>."},"article_type":"original","type":"journal_article","scopus_import":"1","date_created":"2021-08-08T22:01:25Z","publication":"Quantum Science and Technology","oa_version":"Published Version","status":"public","has_accepted_license":"1","external_id":{"arxiv":["2008.08764"],"isi":["000673081500001"]},"abstract":[{"text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.","lang":"eng"}],"volume":6,"issue":"4","month":"07","year":"2021","publication_status":"published","file_date_updated":"2021-08-09T12:23:13Z","author":[{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"last_name":"Lambert","first_name":"Nicholas J.","full_name":"Lambert, Nicholas J."},{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"full_name":"Schwefel, Harald G.L.","last_name":"Schwefel","first_name":"Harald G.L."}],"isi":1,"file":[{"content_type":"application/pdf","date_created":"2021-08-09T12:23:13Z","access_level":"open_access","creator":"cchlebak","relation":"main_file","file_id":"9836","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","date_updated":"2021-08-09T12:23:13Z","checksum":"b15c2c228487a75002c3b52d56f23d5c","file_size":2366118}],"acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","doi":"10.1088/2058-9565/ac0f36","publisher":"IOP Publishing","_id":"9815","quality_controlled":"1","date_published":"2021-07-15T00:00:00Z","article_number":"045005","day":"15","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Thermal noise in electro-optic devices at cryogenic temperatures","oa":1,"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2058-9565"]}},{"pmid":1,"author":[{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Hledik"},{"full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova"},{"first_name":"Mathias","last_name":"Beiglböck","full_name":"Beiglböck, Mathias"},{"full_name":"Herdina, Anna Nele","last_name":"Herdina","first_name":"Anna Nele"},{"full_name":"Strassl, Robert","last_name":"Strassl","first_name":"Robert"},{"full_name":"Posch, Martin","last_name":"Posch","first_name":"Martin"}],"month":"07","volume":16,"issue":"7","publication_status":"published","file_date_updated":"2021-08-09T11:52:14Z","year":"2021","language":[{"iso":"eng"}],"citation":{"mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &#38; Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>."},"article_type":"original","status":"public","has_accepted_license":"1","external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"type":"journal_article","publication":"PLoS ONE","date_created":"2021-08-08T22:01:26Z","oa_version":"Published Version","scopus_import":"1","ddc":["610"],"date_updated":"2023-08-10T14:26:32Z","intvolume":"        16","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1932-6203"]},"article_processing_charge":"Yes","department":[{"_id":"NiBa"}],"day":"29","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e0255267","_id":"9816","date_published":"2021-07-29T00:00:00Z","quality_controlled":"1","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0255267","isi":1,"acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","file":[{"relation":"main_file","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","date_created":"2021-08-09T11:52:14Z","file_size":773921,"checksum":"ae4df60eb62f4491278588548d0c1f93","success":1,"date_updated":"2021-08-09T11:52:14Z","file_name":"2021_PLoSONE_Hledík.pdf","file_id":"9835"}]},{"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mechanics-aware deformation of yarn pattern geometry","oa":1,"day":"01","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"quality_controlled":"1","_id":"9818","date_published":"2021-08-01T00:00:00Z","article_number":"168","doi":"10.1145/3450626.3459816","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","isi":1,"publisher":"Association for Computing Machinery","author":[{"full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl","first_name":"Georg"},{"last_name":"Narain","first_name":"Rahul","full_name":"Narain, Rahul"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2021","publication_status":"published","volume":40,"related_material":{"record":[{"relation":"software","status":"public","id":"9327"},{"status":"public","id":"12358","relation":"dissertation_contains"}],"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/"}]},"issue":"4","month":"08","main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"type":"journal_article","oa_version":"Published Version","publication":"ACM Transactions on Graphics","date_created":"2021-08-08T22:01:27Z","scopus_import":"1","status":"public","external_id":{"isi":["000674930900132"]},"abstract":[{"lang":"eng","text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales."}],"language":[{"iso":"eng"}],"citation":{"short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>."},"article_type":"original","ec_funded":1,"intvolume":"        40","ddc":["000"],"date_updated":"2026-06-18T19:57:47Z","project":[{"grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}]},{"article_number":"44","quality_controlled":"1","_id":"9819","date_published":"2021-08-01T00:00:00Z","publisher":"Association for Computing Machinery","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","file":[{"success":1,"checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","date_updated":"2021-08-09T11:41:50Z","file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf","file_id":"9834","file_size":49840741,"date_created":"2021-08-09T11:41:50Z","content_type":"application/pdf","relation":"main_file","creator":"asandaue","access_level":"open_access"}],"doi":"10.1145/3450626.3459765","isi":1,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"BeBi"}],"day":"01","oa":1,"title":"PhotoApp: Photorealistic appearance editing of head portraits","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>","ieee":"B. R. Mallikarjun <i>et al.</i>, “PhotoApp: Photorealistic appearance editing of head portraits,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021).","chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>."},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates."}],"status":"public","has_accepted_license":"1","external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"date_created":"2021-08-08T22:01:27Z","publication":"ACM Transactions on Graphics","oa_version":"Published Version","scopus_import":"1","type":"journal_article","date_updated":"2026-04-16T08:19:58Z","arxiv":1,"ddc":["000"],"intvolume":"        40","author":[{"last_name":"Mallikarjun","first_name":"B. R.","full_name":"Mallikarjun, B. R."},{"last_name":"Tewari","first_name":"Ayush","full_name":"Tewari, Ayush"},{"full_name":"Dib, Abdallah","first_name":"Abdallah","last_name":"Dib"},{"last_name":"Weyrich","first_name":"Tim","full_name":"Weyrich, Tim"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"},{"full_name":"Seidel, Hans Peter","first_name":"Hans Peter","last_name":"Seidel"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"first_name":"Louis","last_name":"Chevallier","full_name":"Chevallier, Louis"},{"full_name":"Elgharib, Mohamed A.","first_name":"Mohamed A.","last_name":"Elgharib"},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"month":"08","issue":"4","volume":40,"publication_status":"published","file_date_updated":"2021-08-09T11:41:50Z","year":"2021"},{"publication_status":"published","year":"2021","month":"08","volume":40,"issue":"4","author":[{"first_name":"Ana","last_name":"Serrano","full_name":"Serrano, Ana"},{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"last_name":"Wang","first_name":"Chao","full_name":"Wang, Chao"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","last_name":"Piovarci","first_name":"Michael","orcid":"0000-0002-5062-4474"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"}],"date_updated":"2026-04-16T08:20:28Z","intvolume":"        40","status":"public","external_id":{"isi":["000674930900090"]},"abstract":[{"lang":"eng","text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design."}],"main_file_link":[{"open_access":"1","url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf"}],"type":"journal_article","oa_version":"Submitted Version","publication":"ACM Transactions on Graphics","scopus_import":"1","date_created":"2021-08-08T22:01:28Z","language":[{"iso":"eng"}],"citation":{"apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &#38; Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.","ieee":"A. Serrano <i>et al.</i>, “The effect of shape and illumination on material perception: Model and applications,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021).","chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>."},"article_type":"original","title":"The effect of shape and illumination on material perception: Model and applications","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"BeBi"}],"day":"01","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"article_processing_charge":"No","publisher":"Association for Computing Machinery","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","doi":"10.1145/3450626.3459813","isi":1,"article_number":"125","_id":"9820","quality_controlled":"1","date_published":"2021-08-01T00:00:00Z"},{"publication_status":"published","file_date_updated":"2021-08-09T09:25:41Z","year":"2021","month":"07","volume":16,"issue":"7","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","last_name":"Graff","first_name":"Beata"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel"},{"id":"4483EF78-F248-11E8-B48F-1D18A9856A87","full_name":"Jablonski, Grzegorz","last_name":"Jablonski","first_name":"Grzegorz","orcid":"0000-0002-3536-9866"},{"full_name":"Gąsecki, Dariusz","first_name":"Dariusz","last_name":"Gąsecki"},{"last_name":"Narkiewicz","first_name":"Krzysztof","full_name":"Narkiewicz, Krzysztof"}],"pmid":1,"ddc":["006"],"date_updated":"2026-04-02T13:56:42Z","intvolume":"        16","external_id":{"isi":["000678124900050"],"pmid":["34292957"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode."}],"type":"journal_article","oa_version":"Published Version","date_created":"2021-08-08T22:01:28Z","publication":"PLoS ONE","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","citation":{"ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>.","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>."},"title":"Persistent homology as a new method of the assessment of heart rate variability","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"HeEd"}],"day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1932-6203"]},"article_processing_charge":"Yes","publisher":"Public Library of Science","isi":1,"doi":"10.1371/journal.pone.0253851","acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","file":[{"success":1,"checksum":"0277aa155d5db1febd2cb384768bba5f","file_id":"9832","file_name":"2021_PLoSONE_Graff.pdf","date_updated":"2021-08-09T09:25:41Z","file_size":2706919,"content_type":"application/pdf","date_created":"2021-08-09T09:25:41Z","creator":"asandaue","relation":"main_file","access_level":"open_access"}],"article_number":"e0253851","_id":"9821","date_published":"2021-07-01T00:00:00Z","quality_controlled":"1"}]