[{"file_date_updated":"2023-07-18T09:18:55Z","author":[{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"Elefante","full_name":"Elefante, Stefano"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"}],"date_created":"2023-06-23T11:01:23Z","date_updated":"2023-07-18T09:30:54Z","year":"2023","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publisher":"EuroCC","publication_status":"inpress","month":"07","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","start_date":"2023-06-13","end_date":"2023-06-15"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","type":"conference_abstract","file":[{"date_created":"2023-07-18T09:18:55Z","date_updated":"2023-07-18T09:18:55Z","success":1,"checksum":"ec8e4295d54171032cdd1b01423eb4a6","file_id":"13249","relation":"main_file","creator":"dernst","file_size":316959,"content_type":"application/pdf","file_name":"2023_ASHPC_Schloegl.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13161","status":"public","ddc":["000"],"title":"Running Windows-applications on a Linux HPC cluster using WINE","has_accepted_license":"1","article_processing_charge":"No","day":"01","date_published":"2023-07-01T00:00:00Z","citation":{"ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.","apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d."},"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","page":"59-59"},{"article_type":"original","page":"6309-6314","publication":"The Journal of Physical Chemistry Letters","citation":{"chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158"},"date_published":"2023-07-05T00:00:00Z","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"day":"05","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","status":"public","ddc":["530"],"intvolume":" 14","_id":"13251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"13253","date_created":"2023-07-19T06:55:39Z","date_updated":"2023-07-19T06:55:39Z","checksum":"c0c040063f06a51b9c463adc504f1a23","success":1,"file_name":"2023_JourPhysChemistry_Wei.pdf","access_level":"open_access","file_size":2121252,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy."}],"issue":"27","isi":1,"quality_controlled":"1","project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/acs.jpclett.3c01158","month":"07","publication_identifier":{"eissn":["1948-7185"]},"publication_status":"published","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"publisher":"American Chemical Society","year":"2023","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","date_updated":"2023-07-19T06:59:19Z","date_created":"2023-07-18T11:13:17Z","volume":14,"author":[{"full_name":"Wei, Yujing","first_name":"Yujing","last_name":"Wei","id":"0c5ff007-2600-11ee-b896-98bd8d663294","orcid":"0000-0001-8913-9719"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"}],"file_date_updated":"2023-07-19T06:55:39Z","ec_funded":1},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.03447"]},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.ICALP.2023.129","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959772785"],"eissn":["1868-8969"]},"month":"07","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kebis, Pavol","first_name":"Pavol","last_name":"Kebis"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","first_name":"Nicolas Adrien"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"volume":261,"date_updated":"2023-07-31T08:38:38Z","date_created":"2023-07-24T15:11:41Z","ec_funded":1,"file_date_updated":"2023-07-24T15:11:05Z","citation":{"short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20."},"publication":"50th International Colloquium on Automata, Languages, and Programming","page":"129:1--129:20","date_published":"2023-07-05T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes","day":"05","_id":"13292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 261","status":"public","ddc":["000"],"title":"Regular methods for operator precedence languages","file":[{"creator":"esarac","file_size":859379,"content_type":"application/pdf","file_name":"icalp23.pdf","access_level":"open_access","date_updated":"2023-07-24T15:11:05Z","date_created":"2023-07-24T15:11:05Z","success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2","file_id":"13293","relation":"main_file"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}]},{"date_published":"2023-04-14T00:00:00Z","article_type":"original","citation":{"ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029."},"publication":"SciPost Physics Core","has_accepted_license":"1","article_processing_charge":"No","day":"14","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"oa_version":"Published Version","file":[{"success":1,"checksum":"b472bc82108747eda5d52adf9e2ac7f3","date_updated":"2023-07-31T09:02:27Z","date_created":"2023-07-31T09:02:27Z","file_id":"13329","relation":"main_file","creator":"dernst","file_size":523236,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_SciPostPhysCore_Tucci.pdf"}],"intvolume":" 6","title":"Stochastic representation of the quantum quartic oscillator","status":"public","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13277","issue":"2","abstract":[{"text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.21468/scipostphyscore.6.2.029","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","external_id":{"arxiv":["2211.01923"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2666-9366"]},"month":"04","volume":6,"date_created":"2023-07-24T10:47:46Z","date_updated":"2023-07-31T09:03:28Z","author":[{"last_name":"Tucci","first_name":"Gennaro","full_name":"Tucci, Gennaro"},{"full_name":"De Nicola, Stefano","first_name":"Stefano","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4842-6671"},{"full_name":"Wald, Sascha","last_name":"Wald","first_name":"Sascha"},{"first_name":"Andrea","last_name":"Gambassi","full_name":"Gambassi, Andrea"}],"publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","year":"2023","ec_funded":1,"file_date_updated":"2023-07-31T09:02:27Z","article_number":"029"},{"doi":"10.21468/scipostphyscodeb.12","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2202.04603"]},"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"month":"04","publication_identifier":{"issn":["2949-804X"]},"author":[{"first_name":"Lukas","last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas"},{"full_name":"Huber, David","first_name":"David","last_name":"Huber"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13275"}]},"date_updated":"2023-07-31T09:16:02Z","date_created":"2023-07-24T10:47:15Z","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","year":"2023","publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"MiLe"}],"file_date_updated":"2023-07-31T09:09:23Z","ec_funded":1,"article_number":"12","date_published":"2023-04-19T00:00:00Z","publication":"SciPost Physics Codebases","citation":{"ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12.","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023)."},"article_type":"original","day":"19","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":551418,"file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","access_level":"open_access","date_updated":"2023-07-31T09:09:23Z","date_created":"2023-07-31T09:09:23Z","success":1,"checksum":"f583a70fe915d2208c803f5afb426daa","file_id":"13330","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13276","ddc":["530"],"status":"public","title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"type":"journal_article"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"ec_funded":1,"year":"2023","_id":"13275","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"status":"public","title":"Codebase release 1.0 for FermiFCI","publisher":"SciPost Foundation","department":[{"_id":"MiLe"}],"author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"last_name":"Huber","first_name":"David","full_name":"Huber, David"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"related_material":{"record":[{"id":"13276","status":"public","relation":"used_in_publication"}]},"date_created":"2023-07-24T10:46:23Z","date_updated":"2023-07-31T09:16:02Z","oa_version":"Published Version","month":"04","day":"19","article_processing_charge":"No","oa":1,"citation":{"chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0.","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0"},"main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.21468/scipostphyscodeb.12-r1.0","date_published":"2023-04-19T00:00:00Z"},{"author":[{"last_name":"Fedorov","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander"},{"last_name":"Hashemi","first_name":"Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","full_name":"Hashemi, Diba"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"date_updated":"2023-07-31T10:54:32Z","date_created":"2023-07-23T22:01:12Z","year":"2023","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","publication_status":"published","file_date_updated":"2023-07-31T10:53:08Z","doi":"10.1145/3558481.3591082","conference":{"location":"Orlando, FL, United States","start_date":"2023-06-17","end_date":"2023-06-19","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2304.09331"]},"oa":1,"quality_controlled":"1","publication_identifier":{"isbn":["9781450395458"]},"month":"06","file":[{"relation":"main_file","file_id":"13334","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-31T10:53:08Z","access_level":"open_access","file_name":"2023_SPAA_Fedorov.pdf","file_size":2087937,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13262","title":"Provably-efficient and internally-deterministic parallel Union-Find","status":"public","ddc":["000"],"abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"type":"conference","date_published":"2023-06-17T00:00:00Z","citation":{"chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082"},"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","page":"261-271","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"17","scopus_import":"1"},{"type":"journal_article","issue":"2","abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"intvolume":" 16","ddc":["576"],"status":"public","title":"Ten years of demographic modelling of divergence and speciation in the sea","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11479","file":[{"success":1,"checksum":"d4d6fa9ddf36643af994a6a757919afb","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","file_id":"12685","relation":"main_file","creator":"dernst","file_size":2269822,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_EvolutionaryApplications_DeJode.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"542-559","article_type":"original","citation":{"ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428."},"publication":"Evolutionary Applications","date_published":"2023-02-01T00:00:00Z","file_date_updated":"2023-02-27T07:10:17Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","year":"2023","volume":16,"date_created":"2022-07-03T22:01:33Z","date_updated":"2023-08-01T12:25:44Z","author":[{"first_name":"Aurélien","last_name":"De Jode","full_name":"De Jode, Aurélien"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"publication_identifier":{"eissn":["1752-4571"]},"month":"02","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000815663700001"]},"language":[{"iso":"eng"}],"doi":"10.1111/eva.13428"},{"date_published":"2023-01-10T00:00:00Z","citation":{"ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9."},"publication":"Scientific Reports","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"10","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12336","date_updated":"2023-01-23T07:53:23Z","date_created":"2023-01-23T07:53:23Z","checksum":"a8b83739f4a951e83e0b2a778f03b327","success":1,"file_name":"2023_ScientificReports_Gomez.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2167792,"creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12329","intvolume":" 13","status":"public","title":"New approaches to epidemic modeling on networks","ddc":["510"],"abstract":[{"text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41598-022-19827-9","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001003345000051"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2045-2322"]},"month":"01","author":[{"last_name":"Gómez","first_name":"Arturo","full_name":"Gómez, Arturo"},{"first_name":"Goncalo","last_name":"Oliveira","id":"58abbde8-f455-11eb-a497-98c8fd71b905","full_name":"Oliveira, Goncalo"}],"volume":13,"date_updated":"2023-08-01T12:31:40Z","date_created":"2023-01-22T23:00:55Z","year":"2023","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2023-01-23T07:53:23Z","article_number":"468"},{"intvolume":" 2023","title":"Integral points of bounded height on a log Fano threefold","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9034","oa_version":"Preprint","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"page":"6780-6808","article_type":"original","citation":{"short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808."},"publication":"International Mathematics Research Notices","date_published":"2023-04-01T00:00:00Z","article_processing_charge":"No","day":"01","publisher":"Oxford Academic","department":[{"_id":"TiBr"}],"publication_status":"published","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","year":"2023","volume":2023,"date_created":"2021-01-22T09:31:09Z","date_updated":"2023-08-01T12:23:55Z","author":[{"full_name":"Wilsch, Florian Alexander","first_name":"Florian Alexander","last_name":"Wilsch","id":"560601DA-8D36-11E9-A136-7AC1E5697425","orcid":"0000-0001-7302-8256"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1901.08503"],"isi":["000773116000001"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnac048","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"month":"04"},{"type":"journal_article","abstract":[{"text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.","lang":"eng"}],"intvolume":" 14","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12469","file":[{"success":1,"checksum":"cd52292963acce1111634d9fac08c699","date_updated":"2023-04-17T07:49:09Z","date_created":"2023-04-17T07:49:09Z","file_id":"12843","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4866332,"access_level":"open_access","file_name":"2023_FrontMicrobiology_Viljakainen.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"16","article_type":"original","citation":{"chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002"},"publication":"Frontiers in Microbiology","date_published":"2023-03-16T00:00:00Z","article_number":"1119002","file_date_updated":"2023-04-17T07:49:09Z","publisher":"Frontiers","department":[{"_id":"SyCr"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","volume":14,"date_updated":"2023-08-01T12:39:58Z","date_created":"2023-01-31T08:13:40Z","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","first_name":"Matthias","last_name":"Fürst","full_name":"Fürst, Matthias"},{"first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"full_name":"Jurvansuu, Jaana","first_name":"Jaana","last_name":"Jurvansuu"},{"full_name":"Oh, Jinook","orcid":"0000-0001-7425-2372","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","last_name":"Oh","first_name":"Jinook"},{"full_name":"Tolonen, Lassi","last_name":"Tolonen","first_name":"Lassi"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"last_name":"Rattei","first_name":"Thomas","full_name":"Rattei, Thomas"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"publication_identifier":{"eissn":["1664-302X"]},"month":"03","project":[{"grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Viral pathogens and social immunity in ants"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["PPR559293 "],"isi":["000961542100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1119002"},{"_id":"12287","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 69","status":"public","ddc":["510"],"title":"Local criteria for triangulating general manifolds","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","content_type":"application/pdf","file_size":582850,"creator":"dernst","relation":"main_file","file_id":"12488","checksum":"46352e0ee71e460848f88685ca852681","success":1,"date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use."}],"citation":{"chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7"},"publication":"Discrete & Computational Geometry","page":"156-191","article_type":"original","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"article_processing_charge":"No","has_accepted_license":"1","day":"01","year":"2023","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"first_name":"Jean-Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel"},{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"last_name":"Ghosh","first_name":"Arijit","full_name":"Ghosh, Arijit"},{"last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"volume":69,"date_created":"2023-01-16T10:04:06Z","date_updated":"2023-08-01T12:47:32Z","ec_funded":1,"file_date_updated":"2023-02-02T11:01:10Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000862193600001"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00454-022-00431-7","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"01"},{"scopus_import":"1","keyword":["Biochemistry"],"day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Biochemical Society Transactions","citation":{"ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99."},"article_type":"original","page":"87-99","date_published":"2023-02-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"issue":"1","_id":"12421","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","status":"public","intvolume":" 51","oa_version":"Published Version","file":[{"date_updated":"2023-03-16T07:58:16Z","date_created":"2023-03-16T07:58:16Z","checksum":"4e7069845e3dad22bb44fb71ec624c60","success":1,"relation":"main_file","file_id":"12728","file_size":10045006,"content_type":"application/pdf","creator":"dernst","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","access_level":"open_access"}],"month":"02","publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000926043100001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"doi":"10.1042/bst20220221","language":[{"iso":"eng"}],"file_date_updated":"2023-03-16T07:58:16Z","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","year":"2023","publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Portland Press","author":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"full_name":"Javoor, Manjunath","last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"date_updated":"2023-08-01T12:55:32Z","date_created":"2023-01-27T10:08:19Z","volume":51},{"abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":1931647,"creator":"dernst","access_level":"open_access","file_name":"2023_JourFluidMechanics_Marensi.pdf","checksum":"9224f987caefe5dd85a70814d3cce65c","success":1,"date_updated":"2023-02-02T12:34:54Z","date_created":"2023-02-02T12:34:54Z","relation":"main_file","file_id":"12489"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12105","intvolume":" 954","status":"public","ddc":["530"],"title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"10","scopus_import":"1","date_published":"2023-01-10T00:00:00Z","citation":{"chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001"},"publication":"Journal of Fluid Mechanics","article_type":"original","file_date_updated":"2023-02-02T12:34:54Z","article_number":"A10","author":[{"full_name":"Marensi, Elena","first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"full_name":"Yalniz, Gökhan","first_name":"Gökhan","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"}],"volume":954,"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-01T12:53:23Z","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","year":"2023","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"month":"01","doi":"10.1017/jfm.2022.1001","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2101.07516"],"isi":["000903336600001"]},"oa":1,"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1093/evolut/qpac004","isi":1,"quality_controlled":"1","external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"publication_identifier":{"eissn":["1558-5646"]},"month":"01","volume":77,"date_created":"2023-02-05T23:00:59Z","date_updated":"2023-08-01T12:58:30Z","author":[{"full_name":"Bolnick, Daniel I.","first_name":"Daniel I.","last_name":"Bolnick"},{"full_name":"Hund, Amanda K.","first_name":"Amanda K.","last_name":"Hund"},{"full_name":"Nosil, Patrik","last_name":"Nosil","first_name":"Patrik"},{"full_name":"Peng, Foen","last_name":"Peng","first_name":"Foen"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"last_name":"Subramanian","first_name":"Swapna","full_name":"Subramanian, Swapna"},{"full_name":"Wolf, Jochen B.W.","last_name":"Wolf","first_name":"Jochen B.W."},{"full_name":"Yukilevich, Roman","last_name":"Yukilevich","first_name":"Roman"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","date_published":"2023-01-01T00:00:00Z","page":"318-328","article_type":"original","citation":{"mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023."},"publication":"Evolution: International journal of organic evolution","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","intvolume":" 77","status":"public","title":"A multivariate view of the speciation continuum","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12514","issue":"1","abstract":[{"lang":"eng","text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model."}],"type":"journal_article"},{"day":"08","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-02-08T00:00:00Z","publication":"2022 IEEE International Conference on Data Mining Workshops","citation":{"apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093."},"abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"type":"conference","file":[{"checksum":"c253bee25e6dfe484f96662daa119cb6","success":1,"date_updated":"2023-02-14T07:58:26Z","date_created":"2023-02-14T07:58:26Z","relation":"main_file","file_id":"12549","file_size":1183339,"content_type":"application/pdf","creator":"fkarimip","access_level":"open_access","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf"}],"oa_version":"Submitted Version","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","ddc":["600"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12548","month":"02","publication_identifier":{"eissn":["2375-9259"],"eisbn":["9798350346091"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2022-12-01","location":"Orlando, FL, United States","start_date":"2022-11-28","name":"ICDMW: Conference on Data Mining Workshops"},"doi":"10.1109/icdmw58026.2022.00093","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000971492200145"]},"file_date_updated":"2023-02-14T07:58:26Z","article_number":"00093","date_updated":"2023-08-01T13:15:48Z","date_created":"2023-02-14T07:56:21Z","author":[{"first_name":"Mohammad","last_name":"Forghani","full_name":"Forghani, Mohammad"},{"full_name":"Claramunt, Christophe","last_name":"Claramunt","first_name":"Christophe"},{"orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","last_name":"Karimipour","first_name":"Farid","full_name":"Karimipour, Farid"},{"first_name":"Georg","last_name":"Heiler","full_name":"Heiler, Georg"}],"publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"HeEd"}],"year":"2023"},{"doi":"10.1137/20m1378223","language":[{"iso":"eng"}],"external_id":{"arxiv":["2003.11351"],"isi":["000955000000001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"oa":1,"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"month":"01","author":[{"first_name":"Andrei","last_name":"Krokhin","full_name":"Krokhin, Andrei"},{"full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456","id":"ec596741-c539-11ec-b829-c79322a91242","last_name":"Opršal","first_name":"Jakub"},{"full_name":"Wrochna, Marcin","first_name":"Marcin","last_name":"Wrochna"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"volume":52,"date_created":"2023-02-16T07:03:52Z","date_updated":"2023-08-01T13:11:30Z","year":"2023","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","department":[{"_id":"UlWa"}],"publisher":"Society for Industrial & Applied Mathematics","publication_status":"published","ec_funded":1,"date_published":"2023-01-01T00:00:00Z","citation":{"ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79."},"publication":"SIAM Journal on Computing","page":"38-79","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["General Mathematics","General Computer Science"],"oa_version":"Preprint","_id":"12563","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 52","title":"Topology and adjunction in promise constraint satisfaction","status":"public","issue":"1","abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"type":"journal_article"},{"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.107.014608","month":"01","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication_status":"published","department":[{"_id":"GradSch"}],"publisher":"American Physical Society","year":"2023","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","date_updated":"2023-08-01T13:09:45Z","date_created":"2023-02-12T23:00:59Z","volume":107,"author":[{"id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","first_name":"Mauricio Nicolas","last_name":"Rojas Vega","full_name":"Rojas Vega, Mauricio Nicolas"},{"first_name":"Pablo","last_name":"De Castro","full_name":"De Castro, Pablo"},{"full_name":"Soto, Rodrigo","first_name":"Rodrigo","last_name":"Soto"}],"article_number":"014608","article_type":"original","publication":"Physical Review E","citation":{"ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608."},"date_published":"2023-01-24T00:00:00Z","scopus_import":"1","day":"24","article_processing_charge":"No","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","status":"public","intvolume":" 107","_id":"12545","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.","lang":"eng"}],"issue":"1"},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Proceedings of the American Mathematical Society","citation":{"ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239.","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914."},"article_type":"original","page":"907-914","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent.","lang":"eng"}],"issue":"3","_id":"12427","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","intvolume":" 151","oa_version":"Preprint","month":"01","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03013498/"}],"external_id":{"isi":["000898440000001"]},"isi":1,"quality_controlled":"1","doi":"10.1090/proc/15239","language":[{"iso":"eng"}],"year":"2023","publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"American Mathematical Society","author":[{"id":"3ACCD756-F248-11E8-B48F-1D18A9856A87","first_name":"Francesca","last_name":"Balestrieri","full_name":"Balestrieri, Francesca"}],"date_created":"2023-01-29T23:00:58Z","date_updated":"2023-08-01T13:03:32Z","volume":151},{"language":[{"iso":"eng"}],"doi":"10.3390/ijms24032128","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000930324700001"]},"publication_identifier":{"eissn":["1422-0067"]},"month":"01","volume":24,"date_updated":"2023-08-01T13:16:36Z","date_created":"2023-02-19T23:00:56Z","author":[{"full_name":"Mrestani, Achmed","first_name":"Achmed","last_name":"Mrestani"},{"last_name":"Lichter","first_name":"Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","full_name":"Lichter, Katharina"},{"last_name":"Sirén","first_name":"Anna Leena","full_name":"Sirén, Anna Leena"},{"full_name":"Heckmann, Manfred","first_name":"Manfred","last_name":"Heckmann"},{"full_name":"Paul, Mila M.","first_name":"Mila M.","last_name":"Paul"},{"full_name":"Pauli, Martin","first_name":"Martin","last_name":"Pauli"}],"publisher":"MDPI","department":[{"_id":"PeJo"}],"publication_status":"published","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","year":"2023","file_date_updated":"2023-02-20T07:09:27Z","article_number":"2128","date_published":"2023-01-21T00:00:00Z","article_type":"original","citation":{"short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128."},"publication":"International Journal of Molecular Sciences","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2823025,"file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access","date_updated":"2023-02-20T07:09:27Z","date_created":"2023-02-20T07:09:27Z","success":1,"checksum":"69a35dcd3e0249f902ab881b06ee2e58","file_id":"12569","relation":"main_file"}],"intvolume":" 24","status":"public","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12567","issue":"3","abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}],"type":"journal_article"}]