[{"file":[{"success":1,"content_type":"application/pdf","date_updated":"2020-11-26T18:47:58Z","access_level":"open_access","file_size":7618987,"file_name":"Full_manuscript_with_SI_opt_red.pdf","file_id":"8820","checksum":"658ba90979ca9528a2efdfac8547047a","relation":"main_file","date_created":"2020-11-26T18:47:58Z","creator":"lsazanov"}],"publisher":"American Association for the Advancement of Science","pmid":1,"scopus_import":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"article_type":"original","date_created":"2020-11-08T23:01:23Z","issue":"6516","file_date_updated":"2020-11-26T18:47:58Z","abstract":[{"text":"Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.","lang":"eng"}],"volume":370,"date_published":"2020-10-30T00:00:00Z","author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen","last_name":"Kampjut","first_name":"Domen"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"day":"30","language":[{"iso":"eng"}],"year":"2020","publication":"Science","ec_funded":1,"isi":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"}],"citation":{"apa":"Kampjut, D., &#38; Sazanov, L. A. (2020). The coupling mechanism of mammalian respiratory complex I. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abc4209\">https://doi.org/10.1126/science.abc4209</a>","mla":"Kampjut, Domen, and Leonid A. Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” <i>Science</i>, vol. 370, no. 6516, eabc4209, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/science.abc4209\">10.1126/science.abc4209</a>.","ama":"Kampjut D, Sazanov LA. The coupling mechanism of mammalian respiratory complex I. <i>Science</i>. 2020;370(6516). doi:<a href=\"https://doi.org/10.1126/science.abc4209\">10.1126/science.abc4209</a>","chicago":"Kampjut, Domen, and Leonid A Sazanov. “The Coupling Mechanism of Mammalian Respiratory Complex I.” <i>Science</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/science.abc4209\">https://doi.org/10.1126/science.abc4209</a>.","short":"D. Kampjut, L.A. Sazanov, Science 370 (2020).","ieee":"D. Kampjut and L. A. Sazanov, “The coupling mechanism of mammalian respiratory complex I,” <i>Science</i>, vol. 370, no. 6516. American Association for the Advancement of Science, 2020.","ista":"Kampjut D, Sazanov LA. 2020. The coupling mechanism of mammalian respiratory complex I. Science. 370(6516), eabc4209."},"article_processing_charge":"No","status":"public","type":"journal_article","title":"The coupling mechanism of mammalian respiratory complex I","_id":"8737","intvolume":"       370","doi":"10.1126/science.abc4209","external_id":{"isi":["000583031800004"],"pmid":["32972993"]},"department":[{"_id":"LeSa"}],"acknowledgement":"We thank J. Novacek (CEITEC Brno) and V.-V. Hodirnau (IST Austria) for their help with collecting cryo-EM datasets. We thank the IST Life Science and Electron Microscopy Facilities for providing equipment. This work has been supported by iNEXT,project number 653706, funded by the Horizon 2020 program of the European Union. This article reflects only the authors’view,and the European Commission is not responsible for any use that may be made of the information it contains. CIISB research infrastructure project LM2015043 funded by MEYS CR is gratefully acknowledged for the financial support of the measurements at the CF Cryo-electron Microscopy and Tomography CEITEC MU.This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement no. 665385","quality_controlled":"1","has_accepted_license":"1","article_number":"eabc4209","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","month":"10","ddc":["572"],"date_updated":"2023-08-22T12:35:38Z","publication_identifier":{"eissn":["10959203"]},"oa":1,"publication_status":"published"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"id":"8563","relation":"research_data","status":"public"}]},"oa_version":"Published Version","month":"10","publication_identifier":{"eissn":["2050084X"]},"date_updated":"2024-02-21T12:43:40Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","article_number":"61106","intvolume":"         9","_id":"8740","external_id":{"isi":["000584369000001"]},"doi":"10.7554/eLife.61106","department":[{"_id":"JoCs"}],"quality_controlled":"1","acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","isi":1,"citation":{"ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. eLife. 9, 61106.","chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.61106\">https://doi.org/10.7554/eLife.61106</a>.","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.61106\">10.7554/eLife.61106</a>","short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, ELife 9 (2020).","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., &#38; Csicsvari, J. L. (2020). Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.61106\">https://doi.org/10.7554/eLife.61106</a>","mla":"Gridchyn, Igor, et al. “Optogenetic Inhibition-Mediated Activity-Dependent Modification of CA1 Pyramidal-Interneuron Connections during Behavior.” <i>ELife</i>, vol. 9, 61106, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.61106\">10.7554/eLife.61106</a>."},"article_processing_charge":"No","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior","year":"2020","language":[{"iso":"eng"}],"day":"05","publication":"eLife","file_date_updated":"2020-11-09T09:17:40Z","date_published":"2020-10-05T00:00:00Z","abstract":[{"lang":"eng","text":"In vitro work revealed that excitatory synaptic inputs to hippocampal inhibitory interneurons could undergo Hebbian, associative, or non-associative plasticity. Both behavioral and learning-dependent reorganization of these connections has also been demonstrated by measuring spike transmission probabilities in pyramidal cell-interneuron spike cross-correlations that indicate monosynaptic connections. Here we investigated the activity-dependent modification of these connections during exploratory behavior in rats by optogenetically inhibiting pyramidal cell and interneuron subpopulations. Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells."}],"volume":9,"author":[{"orcid":"0000-0002-1807-1929","first_name":"Igor","last_name":"Gridchyn","full_name":"Gridchyn, Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schönenberger","first_name":"Philipp","full_name":"Schönenberger, Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Joseph","last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph"},{"last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FWF","grant_number":"I2072-B27","name":"Interneuron plasticity during spatial learning","_id":"257D4372-B435-11E9-9278-68D0E5697425"},{"_id":"2654F984-B435-11E9-9278-68D0E5697425","name":"Interneuro Plasticity During Spatial Learning","call_identifier":"FWF","grant_number":"I03713"}],"article_type":"original","date_created":"2020-11-08T23:01:25Z","file":[{"relation":"main_file","checksum":"6a7b0543c440f4c000a1864e69377d95","date_created":"2020-11-09T09:17:40Z","creator":"dernst","file_id":"8749","access_level":"open_access","file_size":447669,"file_name":"2020_eLife_Gridchyn.pdf","content_type":"application/pdf","date_updated":"2020-11-09T09:17:40Z","success":1}],"publisher":"eLife Sciences Publications","scopus_import":"1"},{"date_created":"2020-11-08T23:01:25Z","article_type":"original","scopus_import":"1","publisher":"The Royal Society","file":[{"access_level":"open_access","file_size":1611485,"file_name":"2020_RoyalSocOpenScience_Klose.pdf","content_type":"application/pdf","date_updated":"2020-11-09T09:07:11Z","checksum":"5505c445de373bfd836eb4d3b48b1f37","relation":"main_file","date_created":"2020-11-09T09:07:11Z","creator":"dernst","file_id":"8748","success":1}],"day":"01","year":"2020","language":[{"iso":"eng"}],"publication":"Royal Society Open Science","volume":7,"abstract":[{"lang":"eng","text":"In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions\r\non the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of\r\nthese qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements."}],"date_published":"2020-06-01T00:00:00Z","author":[{"last_name":"Klose","first_name":"Ann Kristin","full_name":"Klose, Ann Kristin"},{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker","first_name":"Volker","last_name":"Karle","orcid":"0000-0002-6963-0129"},{"first_name":"Ricarda","last_name":"Winkelmann","full_name":"Winkelmann, Ricarda"},{"full_name":"Donges, Jonathan F.","first_name":"Jonathan F.","last_name":"Donges"}],"issue":"6","file_date_updated":"2020-11-09T09:07:11Z","department":[{"_id":"MiLe"}],"acknowledgement":"V.K. thanks the German National Academic Foundation (Studienstiftung des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork (PB.net), the Earth League’s EarthDoc program and the European Research Council Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements. This work has been performed in the context of the copan collaboration and the FutureLab on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments by N. Wunderling, J. Heitzig and M. Wiedermann.","quality_controlled":"1","_id":"8741","intvolume":"         7","doi":"10.1098/rsos.200599","external_id":{"isi":["000545625200001"]},"type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements","isi":1,"article_processing_charge":"No","citation":{"chicago":"Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F. Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” <i>Royal Society Open Science</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsos.200599\">https://doi.org/10.1098/rsos.200599</a>.","ama":"Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. <i>Royal Society Open Science</i>. 2020;7(6). doi:<a href=\"https://doi.org/10.1098/rsos.200599\">10.1098/rsos.200599</a>","short":"A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science 7 (2020).","apa":"Klose, A. K., Karle, V., Winkelmann, R., &#38; Donges, J. F. (2020). Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. <i>Royal Society Open Science</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsos.200599\">https://doi.org/10.1098/rsos.200599</a>","mla":"Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.” <i>Royal Society Open Science</i>, vol. 7, no. 6, 200599, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsos.200599\">10.1098/rsos.200599</a>.","ista":"Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements. Royal Society Open Science. 7(6), 200599.","ieee":"A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements,” <i>Royal Society Open Science</i>, vol. 7, no. 6. The Royal Society, 2020."},"date_updated":"2023-10-18T08:39:17Z","ddc":["530","550"],"publication_identifier":{"eissn":["20545703"]},"publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"06","article_number":"200599","has_accepted_license":"1"},{"intvolume":"        11","_id":"8744","external_id":{"isi":["000592028600001"]},"doi":"10.1038/s41467-020-19372-x","department":[{"_id":"EM-Fac"}],"quality_controlled":"1","acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","isi":1,"citation":{"ieee":"L. Schulte <i>et al.</i>, “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>","short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>, vol. 11, 5569, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>."},"article_processing_charge":"No","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","oa_version":"Published Version","publication_identifier":{"issn":["2041-1723"]},"date_updated":"2023-08-22T12:36:07Z","ddc":["570"],"oa":1,"publication_status":"published","has_accepted_license":"1","article_number":"5569","article_type":"original","date_created":"2020-11-09T07:49:36Z","publisher":"Springer Nature","file":[{"content_type":"application/pdf","date_updated":"2020-11-09T07:56:24Z","file_size":1670898,"access_level":"open_access","file_name":"2020_NatureComm_Schulte.pdf","file_id":"8745","relation":"main_file","checksum":"b2688f0347e69e6629bba582077278c5","date_created":"2020-11-09T07:56:24Z","creator":"dernst","success":1}],"scopus_import":"1","year":"2020","language":[{"iso":"eng"}],"day":"04","publication":"Nature Communications","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"file_date_updated":"2020-11-09T07:56:24Z","date_published":"2020-11-04T00:00:00Z","volume":11,"abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"author":[{"full_name":"Schulte, Linda","first_name":"Linda","last_name":"Schulte"},{"full_name":"Mao, Jiafei","first_name":"Jiafei","last_name":"Mao"},{"last_name":"Reitz","first_name":"Julian","full_name":"Reitz, Julian"},{"last_name":"Sreeramulu","first_name":"Sridhar","full_name":"Sreeramulu, Sridhar"},{"first_name":"Denis","last_name":"Kudlinzki","full_name":"Kudlinzki, Denis"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Meier-Credo","first_name":"Jakob","full_name":"Meier-Credo, Jakob"},{"full_name":"Saxena, Krishna","last_name":"Saxena","first_name":"Krishna"},{"last_name":"Buhr","first_name":"Florian","full_name":"Buhr, Florian"},{"full_name":"Langer, Julian D.","first_name":"Julian D.","last_name":"Langer"},{"full_name":"Blackledge, Martin","last_name":"Blackledge","first_name":"Martin"},{"full_name":"Frangakis, Achilleas S.","last_name":"Frangakis","first_name":"Achilleas S."},{"first_name":"Clemens","last_name":"Glaubitz","full_name":"Glaubitz, Clemens"},{"full_name":"Schwalbe, Harald","last_name":"Schwalbe","first_name":"Harald"}]},{"scopus_import":"1","publisher":"AIP Publishing","main_file_link":[{"url":"https://doi.org/10.1063/5.0025965","open_access":"1"}],"date_created":"2020-11-09T08:05:43Z","article_type":"original","author":[{"full_name":"Miranti, Retno","first_name":"Retno","last_name":"Miranti"},{"full_name":"Septianto, Ricky Dwi","first_name":"Ricky Dwi","last_name":"Septianto"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843"},{"last_name":"Kovalenko","first_name":"Maksym V.","full_name":"Kovalenko, Maksym V."},{"last_name":"Matsushita","first_name":"Nobuhiro","full_name":"Matsushita, Nobuhiro"},{"last_name":"Iwasa","first_name":"Yoshihiro","full_name":"Iwasa, Yoshihiro"},{"first_name":"Satria Zulkarnaen","last_name":"Bisri","full_name":"Bisri, Satria Zulkarnaen"}],"abstract":[{"text":"Research in the field of colloidal semiconductor nanocrystals (NCs) has progressed tremendously, mostly because of their exceptional optoelectronic properties. Core@shell NCs, in which one or more inorganic layers overcoat individual NCs, recently received significant attention due to their remarkable optical characteristics. Reduced Auger recombination, suppressed blinking, and enhanced carrier multiplication are among the merits of core@shell NCs. Despite their importance in device development, the influence of the shell and the surface modification of the core@shell NC assemblies on the charge carrier transport remains a pertinent research objective. Type-II PbTe@PbS core@shell NCs, in which exclusive electron transport was demonstrated, still exhibit instability of their electron \r\n ransport. Here, we demonstrate the enhancement of electron transport and stability in PbTe@PbS core@shell NC assemblies using iodide as a surface passivating ligand. The combination of the PbS shelling and the use of the iodide ligand contributes to the addition of one mobile electron for each core@shell NC. Furthermore, both electron mobility and on/off current modulation ratio values of the core@shell NC field-effect transistor are steady with the usage of iodide. Excellent stability in these exclusively electron-transporting core@shell NCs paves the way for their utilization in electronic devices. ","lang":"eng"}],"volume":117,"date_published":"2020-10-26T00:00:00Z","issue":"17","publication":"Applied Physics Letters","day":"26","year":"2020","language":[{"iso":"eng"}],"title":"Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids","status":"public","type":"journal_article","citation":{"mla":"Miranti, Retno, et al. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” <i>Applied Physics Letters</i>, vol. 117, no. 17, 173101, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/5.0025965\">10.1063/5.0025965</a>.","apa":"Miranti, R., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita, N., Iwasa, Y., &#38; Bisri, S. Z. (2020). Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0025965\">https://doi.org/10.1063/5.0025965</a>","ama":"Miranti R, Septianto RD, Ibáñez M, et al. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. <i>Applied Physics Letters</i>. 2020;117(17). doi:<a href=\"https://doi.org/10.1063/5.0025965\">10.1063/5.0025965</a>","short":"R. Miranti, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita, Y. Iwasa, S.Z. Bisri, Applied Physics Letters 117 (2020).","chicago":"Miranti, Retno, Ricky Dwi Septianto, Maria Ibáñez, Maksym V. Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri. “Electron Transport in Iodide-Capped Core@shell PbTe@PbS Colloidal Nanocrystal Solids.” <i>Applied Physics Letters</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/5.0025965\">https://doi.org/10.1063/5.0025965</a>.","ieee":"R. Miranti <i>et al.</i>, “Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids,” <i>Applied Physics Letters</i>, vol. 117, no. 17. AIP Publishing, 2020.","ista":"Miranti R, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa Y, Bisri SZ. 2020. Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids. Applied Physics Letters. 117(17), 173101."},"article_processing_charge":"No","isi":1,"acknowledgement":"This work was partly supported by Grants-in-Aid for Scientific Research by Young Scientist A (KAKENHI Wakate-A) No.\r\nJP17H04802, Grants-in-Aid for Scientific Research No. JP19H05602 from the Japan Society for the Promotion of Science, and RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID, GA No. 306733) and ETH Zurich via ETH career seed grant (No. SEED-18 16-2). We acknowledge Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission electron microscope facility.","quality_controlled":"1","department":[{"_id":"MaIb"}],"doi":"10.1063/5.0025965","external_id":{"isi":["000591639700001"]},"_id":"8746","intvolume":"       117","article_number":"173101","publication_status":"published","oa":1,"date_updated":"2023-09-05T11:57:23Z","publication_identifier":{"eissn":["1077-3118"],"issn":["0003-6951"]},"month":"10","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_processing_charge":"No","citation":{"ieee":"M. Forets, D. Freire, and C. Schilling, “Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions,” in <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>, Virtual Conference, 2020.","ista":"Forets M, Freire D, Schilling C. 2020. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. 18th ACM-IEEE International Conference on Formal Methods and Models for System Design. MEMOCODE: Conference on Formal Methods and Models for System Design, 9314994.","mla":"Forets, Marcelo, et al. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>, 9314994, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">10.1109/MEMOCODE51338.2020.9314994</a>.","apa":"Forets, M., Freire, D., &#38; Schilling, C. (2020). Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>. Virtual Conference: IEEE. <a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">https://doi.org/10.1109/MEMOCODE51338.2020.9314994</a>","short":"M. Forets, D. Freire, C. Schilling, in:, 18th ACM-IEEE International Conference on Formal Methods and Models for System Design, IEEE, 2020.","ama":"Forets M, Freire D, Schilling C. Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions. In: <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">10.1109/MEMOCODE51338.2020.9314994</a>","chicago":"Forets, Marcelo, Daniel Freire, and Christian Schilling. “Efficient Reachability Analysis of Parametric Linear Hybrid Systems with  Time-Triggered Transitions.” In <i>18th ACM-IEEE International Conference on Formal Methods and Models for System Design</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/MEMOCODE51338.2020.9314994\">https://doi.org/10.1109/MEMOCODE51338.2020.9314994</a>."},"isi":1,"title":"Efficient reachability analysis of parametric linear hybrid systems with  time-triggered transitions","status":"public","type":"conference","doi":"10.1109/MEMOCODE51338.2020.9314994","external_id":{"arxiv":["2006.12325"],"isi":["000661920400013"]},"_id":"8750","quality_controlled":"1","department":[{"_id":"ToHe"}],"arxiv":1,"article_number":"9314994","oa_version":"Preprint","month":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publication_status":"published","conference":{"location":"Virtual Conference","name":"MEMOCODE: Conference on Formal Methods and Models for System Design","start_date":"2020-12-02","end_date":"2020-12-04"},"date_updated":"2023-08-22T12:48:18Z","publication_identifier":{"isbn":["9781728191485"]},"publisher":"IEEE","main_file_link":[{"url":"https://arxiv.org/abs/2006.12325","open_access":"1"}],"scopus_import":"1","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-11-10T07:04:57Z","author":[{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"first_name":"Daniel","last_name":"Freire","full_name":"Freire, Daniel"},{"id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian"}],"abstract":[{"text":"Efficiently handling time-triggered and possibly nondeterministic switches\r\nfor hybrid systems reachability is a challenging task. In this paper we present\r\nan approach based on conservative set-based enclosure of the dynamics that can\r\nhandle systems with uncertain parameters and inputs, where the uncertainties\r\nare bound to given intervals. The method is evaluated on the plant model of an\r\nexperimental electro-mechanical braking system with periodic controller. In\r\nthis model, the fast-switching controller dynamics requires simulation time\r\nscales of the order of nanoseconds. Accurate set-based computations for\r\nrelatively large time horizons are known to be expensive. However, by\r\nappropriately decoupling the time variable with respect to the spatial\r\nvariables, and enclosing the uncertain parameters using interval matrix maps\r\nacting on zonotopes, we show that the computation time can be lowered to 5000\r\ntimes faster with respect to previous works. This is a step forward in formal\r\nverification of hybrid systems because reduced run-times allow engineers to\r\nintroduce more expressiveness in their models with a relatively inexpensive\r\ncomputational cost.","lang":"eng"}],"date_published":"2020-12-04T00:00:00Z","publication":"18th ACM-IEEE International Conference on Formal Methods and Models for System Design","day":"04","year":"2020","language":[{"iso":"eng"}],"ec_funded":1},{"title":"Surpassing the resistance quantum with a geometric superinductor","type":"journal_article","status":"public","citation":{"short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. <i>Physical Review Applied</i>. 2020;14(4). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">10.1103/PhysRevApplied.14.044055</a>","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” <i>Physical Review Applied</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">https://doi.org/10.1103/PhysRevApplied.14.044055</a>.","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., &#38; Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">https://doi.org/10.1103/PhysRevApplied.14.044055</a>","mla":"Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” <i>Physical Review Applied</i>, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.14.044055\">10.1103/PhysRevApplied.14.044055</a>.","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” <i>Physical Review Applied</i>, vol. 14, no. 4. American Physical Society, 2020.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055."},"article_processing_charge":"No","isi":1,"acknowledged_ssus":[{"_id":"NanoFab"}],"acknowledgement":"The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). ","quality_controlled":"1","department":[{"_id":"JoFi"}],"doi":"10.1103/PhysRevApplied.14.044055","external_id":{"isi":["000582797300003"],"arxiv":["2007.01644"]},"_id":"8755","intvolume":"        14","article_number":"044055","has_accepted_license":"1","arxiv":1,"oa":1,"publication_status":"published","ddc":["530"],"date_updated":"2024-08-07T07:11:55Z","publication_identifier":{"eissn":["23317019"]},"oa_version":"Published Version","month":"10","related_material":{"record":[{"relation":"research_data","id":"13070","status":"public"},{"status":"public","relation":"dissertation_contains","id":"9920"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","file":[{"file_size":2607823,"access_level":"open_access","file_name":"2020_PhysReviewApplied_Peruzzo.pdf","content_type":"application/pdf","date_updated":"2021-03-29T11:43:20Z","checksum":"2a634abe75251ae7628cd54c8a4ce2e8","relation":"main_file","date_created":"2021-03-29T11:43:20Z","creator":"dernst","file_id":"9300","success":1}],"publisher":"American Physical Society","project":[{"call_identifier":"FWF","grant_number":"F07105","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"grant_number":"732894","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"}],"article_type":"original","date_created":"2020-11-15T23:01:17Z","author":[{"orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea"},{"full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani","first_name":"Farid"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"volume":14,"abstract":[{"lang":"eng","text":"The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. "}],"date_published":"2020-10-29T00:00:00Z","file_date_updated":"2021-03-29T11:43:20Z","issue":"4","ec_funded":1,"publication":"Physical Review Applied","day":"29","year":"2020","language":[{"iso":"eng"}]},{"quality_controlled":"1","acknowledgement":"The research of A.M. was partially supported by the Deutsche Forschungsgemeinschaft (DFG) via the Collaborative Research Center SFB 1114 Scaling Cascades in Complex Systems (Project No. 235221301), through the Subproject C05 Effective models for materials and interfaces with multiple scales. J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117), and by the Austrian Science Fund (FWF), Project SFB F65. The authors thank Christof Schütte, Robert I. A. Patterson, and Stefanie Winkelmann for helpful and stimulating discussions. Open access funding provided by Austrian Science Fund (FWF).","department":[{"_id":"JaMa"}],"external_id":{"isi":["000587107200002"],"arxiv":["2004.02831"]},"doi":"10.1007/s10955-020-02663-4","intvolume":"       181","page":"2257-2303","_id":"8758","title":"Modeling of chemical reaction systems with detailed balance using gradient structures","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","status":"public","article_processing_charge":"No","citation":{"mla":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” <i>Journal of Statistical Physics</i>, vol. 181, no. 6, Springer Nature, 2020, pp. 2257–303, doi:<a href=\"https://doi.org/10.1007/s10955-020-02663-4\">10.1007/s10955-020-02663-4</a>.","apa":"Maas, J., &#38; Mielke, A. (2020). Modeling of chemical reaction systems with detailed balance using gradient structures. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-020-02663-4\">https://doi.org/10.1007/s10955-020-02663-4</a>","ama":"Maas J, Mielke A. Modeling of chemical reaction systems with detailed balance using gradient structures. <i>Journal of Statistical Physics</i>. 2020;181(6):2257-2303. doi:<a href=\"https://doi.org/10.1007/s10955-020-02663-4\">10.1007/s10955-020-02663-4</a>","short":"J. Maas, A. Mielke, Journal of Statistical Physics 181 (2020) 2257–2303.","chicago":"Maas, Jan, and Alexander Mielke. “Modeling of Chemical Reaction Systems with Detailed Balance Using Gradient Structures.” <i>Journal of Statistical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10955-020-02663-4\">https://doi.org/10.1007/s10955-020-02663-4</a>.","ista":"Maas J, Mielke A. 2020. Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics. 181(6), 2257–2303.","ieee":"J. Maas and A. Mielke, “Modeling of chemical reaction systems with detailed balance using gradient structures,” <i>Journal of Statistical Physics</i>, vol. 181, no. 6. Springer Nature, pp. 2257–2303, 2020."},"isi":1,"oa":1,"publication_status":"published","publication_identifier":{"eissn":["15729613"],"issn":["00224715"]},"ddc":["510"],"date_updated":"2023-08-22T13:24:27Z","oa_version":"Published Version","month":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","arxiv":1,"date_created":"2020-11-15T23:01:18Z","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems","grant_number":" F06504","call_identifier":"FWF"}],"article_type":"original","scopus_import":"1","file":[{"creator":"dernst","date_created":"2021-02-04T10:29:11Z","checksum":"bc2b63a90197b97cbc73eccada4639f5","relation":"main_file","file_id":"9087","file_name":"2020_JourStatPhysics_Maas.pdf","access_level":"open_access","file_size":753596,"date_updated":"2021-02-04T10:29:11Z","content_type":"application/pdf","success":1}],"publisher":"Springer Nature","ec_funded":1,"publication":"Journal of Statistical Physics","year":"2020","language":[{"iso":"eng"}],"day":"01","author":[{"first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mielke","first_name":"Alexander","full_name":"Mielke, Alexander"}],"date_published":"2020-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels."}],"volume":181,"file_date_updated":"2021-02-04T10:29:11Z","issue":"6"},{"month":"11","oa_version":"Published Version","day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"8562","status":"public"}],"link":[{"url":"https://github.com/russelmann/cold-glass-acm","relation":"software"}]},"year":"2020","oa":1,"date_updated":"2024-02-21T12:43:22Z","ddc":["000"],"ec_funded":1,"has_accepted_license":"1","file_date_updated":"2020-11-18T10:04:59Z","author":[{"full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","last_name":"Guseinov","orcid":"0000-0001-9819-5077"}],"date_published":"2020-11-23T00:00:00Z","date_created":"2020-11-16T10:47:18Z","doi":"10.15479/AT:ISTA:8761","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767"}],"_id":"8761","department":[{"_id":"BeBi"}],"contributor":[{"contributor_type":"researcher","first_name":"Konstantinos","last_name":"Gavriil"},{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","first_name":"Ruslan","contributor_type":"researcher","orcid":"0000-0001-9819-5077"},{"first_name":"Jesus","last_name":"Perez Rodriguez","contributor_type":"researcher","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","first_name":"Davide","last_name":"Pellis"},{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","contributor_type":"researcher","orcid":"0000-0002-5198-7445","last_name":"Henderson","first_name":"Paul M"},{"last_name":"Rist","first_name":"Florian","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Helmut","last_name":"Pottmann"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","contributor_type":"researcher","orcid":"0000-0001-6511-9385"}],"publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2020-11-16T10:31:29Z","creator":"rguseino","checksum":"f5ae57b97017b9f61081032703361233","relation":"main_file","file_id":"8762","file_name":"mdn_model.tar.gz","file_size":15378270,"access_level":"open_access","date_updated":"2020-11-16T10:31:29Z","content_type":"application/x-gzip","success":1},{"creator":"rguseino","date_created":"2020-11-16T10:43:23Z","relation":"main_file","checksum":"b0d25e04060ee78c585ee2f23542c744","file_id":"8763","file_name":"optimal_panels_data.tar.gz","access_level":"open_access","file_size":615387734,"date_updated":"2020-11-16T10:43:23Z","content_type":"application/x-gzip","success":1},{"checksum":"69c1dde3434ada86d125e0c2588caf1e","relation":"main_file","date_created":"2020-11-18T10:04:59Z","creator":"rguseino","file_id":"8770","access_level":"open_access","file_size":1228,"file_name":"readme.txt","content_type":"text/plain","date_updated":"2020-11-18T10:04:59Z","success":1}],"citation":{"short":"R. Guseinov, (2020).","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>.","ama":"Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">https://doi.org/10.15479/AT:ISTA:8761</a>","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Computational Design of Cold Bent Glass Façades.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8761\">10.15479/AT:ISTA:8761</a>.","ieee":"R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020."},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Supplementary data for \"Computational design of cold bent glass façades\"","type":"research_data","status":"public"},{"citation":{"ieee":"C. Schreck and C. Wojtan, “A practical method for animating anisotropic elastoplastic materials,” <i>Computer Graphics Forum</i>, vol. 39, no. 2. Wiley, pp. 89–99, 2020.","ista":"Schreck C, Wojtan C. 2020. A practical method for animating anisotropic elastoplastic materials. Computer Graphics Forum. 39(2), 89–99.","chicago":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>.","ama":"Schreck C, Wojtan C. A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. 2020;39(2):89-99. doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 39 (2020) 89–99.","apa":"Schreck, C., &#38; Wojtan, C. (2020). A practical method for animating anisotropic elastoplastic materials. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13914\">https://doi.org/10.1111/cgf.13914</a>","mla":"Schreck, Camille, and Chris Wojtan. “A Practical Method for Animating Anisotropic Elastoplastic Materials.” <i>Computer Graphics Forum</i>, vol. 39, no. 2, Wiley, 2020, pp. 89–99, doi:<a href=\"https://doi.org/10.1111/cgf.13914\">10.1111/cgf.13914</a>."},"article_processing_charge":"No","isi":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"A practical method for animating anisotropic elastoplastic materials","status":"public","type":"journal_article","doi":"10.1111/cgf.13914","external_id":{"isi":["000548709600008"]},"page":"89-99","_id":"8765","intvolume":"        39","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would also like to thank Joseph Teran and Chenfanfu Jiang for the helpful discussions.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme under grant agreement No. 638176.","quality_controlled":"1","department":[{"_id":"ChWo"}],"has_accepted_license":"1","oa_version":"Submitted Version","month":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publication_status":"published","date_updated":"2023-09-05T16:00:13Z","ddc":["000"],"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"file":[{"success":1,"content_type":"application/pdf","date_updated":"2020-11-23T09:05:13Z","file_size":38969122,"access_level":"open_access","file_name":"2020_poff_revisited.pdf","file_id":"8796","relation":"main_file","checksum":"7605f605acd84d0942b48bc7a1c2d72e","date_created":"2020-11-23T09:05:13Z","creator":"dernst"}],"publisher":"Wiley","scopus_import":"1","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020"}],"date_created":"2020-11-17T09:35:10Z","article_type":"original","file_date_updated":"2020-11-23T09:05:13Z","issue":"2","author":[{"first_name":"Camille","last_name":"Schreck","full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"abstract":[{"lang":"eng","text":"This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate."}],"volume":39,"date_published":"2020-05-01T00:00:00Z","publication":"Computer Graphics Forum","day":"01","language":[{"iso":"eng"}],"year":"2020","keyword":["Computer Networks and Communications"],"ec_funded":1},{"abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"volume":16,"date_published":"2020-11-05T00:00:00Z","author":[{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"issue":"11","file_date_updated":"2020-11-18T07:26:10Z","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"day":"05","language":[{"iso":"eng"}],"year":"2020","publication":"PLOS Computational Biology","scopus_import":"1","file":[{"success":1,"checksum":"555456dd0e47bcf9e0994bcb95577e88","relation":"main_file","creator":"dernst","date_created":"2020-11-18T07:26:10Z","file_id":"8768","file_size":2498594,"access_level":"open_access","file_name":"2020_PlosCompBio_Kaveh.pdf","content_type":"application/pdf","date_updated":"2020-11-18T07:26:10Z"}],"publisher":"Public Library of Science","date_created":"2020-11-18T07:20:23Z","article_type":"original","article_number":"e1008402","has_accepted_license":"1","date_updated":"2023-08-22T12:49:18Z","ddc":["000"],"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","oa_version":"Published Version","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"The Moran process on 2-chromatic graphs","isi":1,"article_processing_charge":"No","citation":{"ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020.","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>."},"department":[{"_id":"KrCh"}],"acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","quality_controlled":"1","_id":"8767","intvolume":"        16","doi":"10.1371/journal.pcbi.1008402","external_id":{"isi":["000591317200004"]}},{"scopus_import":"1","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.07890"}],"article_type":"original","date_created":"2020-11-18T07:34:17Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas."}],"volume":102,"date_published":"2020-10-01T00:00:00Z","author":[{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp","orcid":"0000-0001-5973-0874"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543"},{"full_name":"Lundholm, D.","first_name":"D.","last_name":"Lundholm"},{"full_name":"Rougerie, N.","last_name":"Rougerie","first_name":"N."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"issue":"14","ec_funded":1,"day":"01","language":[{"iso":"eng"}],"year":"2020","publication":"Physical Review B","type":"journal_article","status":"public","title":"Quantum impurity model for anyons","isi":1,"citation":{"ieee":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” <i>Physical Review B</i>, vol. 102, no. 14. American Physical Society, 2020.","ista":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109.","short":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020).","chicago":"Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>.","ama":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. <i>Physical Review B</i>. 2020;102(14). doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>","mla":"Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>.","apa":"Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., &#38; Seiringer, R. (2020). Quantum impurity model for anyons. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>"},"article_processing_charge":"No","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"acknowledgement":"We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively).","quality_controlled":"1","_id":"8769","intvolume":"       102","doi":"10.1103/physrevb.102.144109","external_id":{"isi":["000582563300001"],"arxiv":["1912.07890"]},"article_number":"144109","arxiv":1,"date_updated":"2023-09-05T12:12:30Z","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","month":"10"},{"ec_funded":1,"language":[{"iso":"eng"}],"year":"2020","day":"13","publication":"Nature Communications","date_published":"2020-11-13T00:00:00Z","abstract":[{"lang":"eng","text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets."}],"volume":11,"author":[{"last_name":"Nicolai","first_name":"Leo","full_name":"Nicolai, Leo"},{"last_name":"Schiefelbein","first_name":"Karin","full_name":"Schiefelbein, Karin"},{"last_name":"Lipsky","first_name":"Silvia","full_name":"Lipsky, Silvia"},{"full_name":"Leunig, Alexander","last_name":"Leunig","first_name":"Alexander"},{"full_name":"Hoffknecht, Marie","first_name":"Marie","last_name":"Hoffknecht"},{"first_name":"Kami","last_name":"Pekayvaz","full_name":"Pekayvaz, Kami"},{"full_name":"Raude, Ben","last_name":"Raude","first_name":"Ben"},{"full_name":"Marx, Charlotte","first_name":"Charlotte","last_name":"Marx"},{"full_name":"Ehrlich, Andreas","first_name":"Andreas","last_name":"Ehrlich"},{"first_name":"Joachim","last_name":"Pircher","full_name":"Pircher, Joachim"},{"full_name":"Zhang, Zhe","last_name":"Zhang","first_name":"Zhe"},{"last_name":"Saleh","first_name":"Inas","full_name":"Saleh, Inas"},{"full_name":"Marel, Anna-Kristina","first_name":"Anna-Kristina","last_name":"Marel"},{"last_name":"Löf","first_name":"Achim","full_name":"Löf, Achim"},{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"last_name":"Lorenz","first_name":"Michael","full_name":"Lorenz, Michael"},{"full_name":"Stark, Konstantin","last_name":"Stark","first_name":"Konstantin"},{"last_name":"Pick","first_name":"Robert","full_name":"Pick, Robert"},{"last_name":"Rosenberger","first_name":"Gerhild","full_name":"Rosenberger, Gerhild"},{"full_name":"Weckbach, Ludwig","first_name":"Ludwig","last_name":"Weckbach"},{"full_name":"Uhl, Bernd","first_name":"Bernd","last_name":"Uhl"},{"last_name":"Xia","first_name":"Sheng","full_name":"Xia, Sheng"},{"full_name":"Reichel, Christoph Andreas","first_name":"Christoph Andreas","last_name":"Reichel"},{"first_name":"Barbara","last_name":"Walzog","full_name":"Walzog, Barbara"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","orcid":"0000-0002-9438-4783"},{"full_name":"Bender, Markus","last_name":"Bender","first_name":"Markus"},{"full_name":"Li, Rong","last_name":"Li","first_name":"Rong"},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"},{"last_name":"Gärtner","first_name":"Florian R","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-11-23T13:29:49Z","article_type":"original","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"747687"}],"date_created":"2020-11-22T23:01:23Z","scopus_import":"1","pmid":1,"publisher":"Springer Nature","file":[{"success":1,"file_name":"2020_NatureComm_Nicolai.pdf","access_level":"open_access","file_size":7035340,"date_updated":"2020-11-23T13:29:49Z","content_type":"application/pdf","creator":"dernst","date_created":"2020-11-23T13:29:49Z","relation":"main_file","checksum":"485b7b6cf30198ba0ce126491a28f125","file_id":"8798"}],"publication_identifier":{"eissn":["20411723"]},"ddc":["570"],"date_updated":"2023-08-22T13:26:26Z","oa":1,"publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-31310-7","relation":"erratum"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"11","article_number":"5778","has_accepted_license":"1","department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"quality_controlled":"1","acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","intvolume":"        11","_id":"8787","external_id":{"isi":["000594648000014"],"pmid":["33188196"]},"doi":"10.1038/s41467-020-19515-0","status":"public","type":"journal_article","title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"citation":{"apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19515-0\">https://doi.org/10.1038/s41467-020-19515-0</a>","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” <i>Nature Communications</i>, vol. 11, 5778, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19515-0\">10.1038/s41467-020-19515-0</a>.","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19515-0\">10.1038/s41467-020-19515-0</a>","chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19515-0\">https://doi.org/10.1038/s41467-020-19515-0</a>.","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","ieee":"L. Nicolai <i>et al.</i>, “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020."},"article_processing_charge":"No"},{"file_date_updated":"2020-11-23T13:06:30Z","issue":"11","author":[{"first_name":"Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria"},{"first_name":"Sabrina","last_name":"Streipert","full_name":"Streipert, Sabrina"},{"last_name":"Filar","first_name":"Jerzy","full_name":"Filar, Jerzy"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"date_published":"2020-11-04T00:00:00Z","abstract":[{"lang":"eng","text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty."}],"volume":8,"publication":"Mathematics","year":"2020","language":[{"iso":"eng"}],"day":"04","ec_funded":1,"publisher":"MDPI","file":[{"success":1,"access_level":"open_access","file_size":565191,"file_name":"2020_Mathematics_Kleshnina.pdf","content_type":"application/pdf","date_updated":"2020-11-23T13:06:30Z","relation":"main_file","checksum":"61cfcc3b35760656ce7a9385a4ace5d2","date_created":"2020-11-23T13:06:30Z","creator":"dernst","file_id":"8797"}],"scopus_import":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"article_type":"original","date_created":"2020-11-22T23:01:24Z","has_accepted_license":"1","article_number":"1945","month":"11","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa":1,"publication_identifier":{"eissn":["22277390"]},"date_updated":"2025-07-14T09:09:49Z","ddc":["000"],"citation":{"ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” <i>Mathematics</i>, vol. 8, no. 11. MDPI, 2020.","apa":"Kleshnina, M., Streipert, S., Filar, J., &#38; Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8111945\">https://doi.org/10.3390/math8111945</a>","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” <i>Mathematics</i>, vol. 8, no. 11, 1945, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8111945\">10.3390/math8111945</a>.","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8111945\">https://doi.org/10.3390/math8111945</a>.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).","ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. <i>Mathematics</i>. 2020;8(11). doi:<a href=\"https://doi.org/10.3390/math8111945\">10.3390/math8111945</a>"},"article_processing_charge":"No","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Prioritised learning in snowdrift-type games","status":"public","type":"journal_article","external_id":{"isi":["000593962100001"]},"doi":"10.3390/math8111945","intvolume":"         8","_id":"8789","quality_controlled":"1","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","department":[{"_id":"KrCh"}]},{"volume":39,"abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"date_published":"2020-11-01T00:00:00Z","author":[{"first_name":"Sergiy","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"last_name":"Frehse","first_name":"Goran","full_name":"Frehse, Goran"},{"first_name":"Kostiantyn","last_name":"Potomkin","full_name":"Potomkin, Kostiantyn"},{"orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian"}],"issue":"11","ec_funded":1,"day":"01","language":[{"iso":"eng"}],"year":"2020","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","scopus_import":"1","publisher":"IEEE","main_file_link":[{"url":"https://arxiv.org/abs/1905.02458","open_access":"1"}],"date_created":"2020-11-22T23:01:25Z","article_type":"original","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"date_updated":"2023-08-22T13:27:33Z","publication_identifier":{"eissn":["19374151"],"issn":["02780070"]},"oa":1,"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","id":"8287","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","oa_version":"Preprint","status":"public","type":"journal_article","title":"Reachability analysis of linear hybrid systems via block decomposition","isi":1,"article_processing_charge":"No","citation":{"ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">https://doi.org/10.1109/TCAD.2020.3012859</a>.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. 2020;39(11):4018-4029. doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">10.1109/TCAD.2020.3012859</a>","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">https://doi.org/10.1109/TCAD.2020.3012859</a>","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">10.1109/TCAD.2020.3012859</a>."},"department":[{"_id":"ToHe"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","quality_controlled":"1","_id":"8790","page":"4018-4029","intvolume":"        39","doi":"10.1109/TCAD.2020.3012859","external_id":{"isi":["000587712700072"],"arxiv":["1905.02458"]}},{"publisher":"Dryad","article_processing_charge":"No","citation":{"mla":"Perini, Samuel, et al. <i>Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","status":"public","type":"research_data_reference","doi":"10.5061/dryad.qrfj6q5cn","date_created":"2020-11-25T11:07:25Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"8809","department":[{"_id":"NiBa"}],"has_accepted_license":"1","author":[{"last_name":"Perini","first_name":"Samuel","full_name":"Perini, Samuel"},{"first_name":"Marina","last_name":"Rafajlovic","full_name":"Rafajlovic, Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}],"date_published":"2020-07-01T00:00:00Z","month":"07","oa_version":"Published Version","day":"01","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","id":"7995","relation":"used_in_publication"}]},"year":"2020","oa":1,"date_updated":"2023-08-22T07:13:37Z"},{"department":[{"_id":"SiHi"}],"_id":"8813","external_id":{"pmid":["PPR234457 "]},"date_created":"2020-11-26T07:17:19Z","doi":"10.1101/2020.11.03.366948","type":"preprint","status":"public","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","citation":{"short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","ieee":"L. Santini <i>et al.</i>, “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"pmid":1,"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","date_updated":"2023-09-12T11:05:28Z","publication_status":"submitted","oa":1,"language":[{"iso":"eng"}],"year":"2020","day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"11","publication":"bioRxiv","date_published":"2020-11-05T00:00:00Z","abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"author":[{"full_name":"Santini, Laura","last_name":"Santini","first_name":"Laura"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"first_name":"Fabian","last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian"},{"full_name":"Suzuki, Toru","first_name":"Toru","last_name":"Suzuki"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"full_name":"Lackner, Andreas","first_name":"Andreas","last_name":"Lackner"},{"first_name":"Nick","last_name":"Warr","full_name":"Warr, Nick"},{"orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"full_name":"Laue, Ernest","first_name":"Ernest","last_name":"Laue"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F.","last_name":"Perry"},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"}]},{"date_created":"2020-12-01T12:38:18Z","publisher":"Institute of Science and Technology Austria","file":[{"file_id":"8919","creator":"jhajny","date_created":"2020-12-04T07:27:52Z","relation":"source_file","checksum":"210a9675af5e4c78b0b56d920ac82866","date_updated":"2021-07-16T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_name":"Jakub Hajný IST Austria final_JH.docx","file_size":91279806,"access_level":"closed"},{"embargo":"2021-12-07","file_id":"8933","relation":"main_file","checksum":"1781385b4aa73eba89cc76c6172f71d2","creator":"jhajny","date_created":"2020-12-09T15:04:41Z","content_type":"application/pdf","date_updated":"2021-12-08T23:30:03Z","file_size":68707697,"access_level":"open_access","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf"}],"supervisor":[{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","language":[{"iso":"eng"}],"day":"01","file_date_updated":"2021-12-08T23:30:03Z","date_published":"2020-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization."}],"author":[{"orcid":"0000-0003-2140-7195","last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"}],"page":"249","_id":"8822","doi":"10.15479/AT:ISTA:8822","department":[{"_id":"JiFr"}],"degree_awarded":"PhD","citation":{"ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","mla":"Hajny, Jakub. <i>Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>.","apa":"Hajny, J. (2020). <i>Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020."},"article_processing_charge":"No","type":"dissertation","status":"public","title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"7427","relation":"part_of_dissertation"},{"id":"6260","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7500","status":"public"},{"status":"public","id":"449","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"191"}]},"oa_version":"Published Version","month":"12","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2025-05-07T11:12:31Z","ddc":["580"],"publication_status":"published","oa":1,"alternative_title":["ISTA Thesis"],"has_accepted_license":"1"},{"project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020"}],"date_created":"2020-12-02T10:42:53Z","file":[{"checksum":"22a612e206232fa94b138b2c2f957582","relation":"main_file","date_created":"2020-12-02T10:42:31Z","creator":"gkatsaro","file_id":"8832","file_size":1697939,"access_level":"open_access","file_name":"Superconducting_2D_Ge.pdf","content_type":"application/pdf","date_updated":"2020-12-02T10:42:31Z"}],"day":"02","year":"2020","language":[{"iso":"eng"}],"publication":"arXiv","ec_funded":1,"file_date_updated":"2020-12-02T10:42:31Z","abstract":[{"text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.","lang":"eng"}],"date_published":"2020-12-02T00:00:00Z","author":[{"id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","last_name":"Aggarwal","orcid":"0000-0001-9985-9293"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C"},{"full_name":"Jirovec, Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"first_name":"Amir","last_name":"Sammak","full_name":"Sammak, Amir"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"first_name":"Sara","last_name":"Marti-Sanchez","full_name":"Marti-Sanchez, Sara"},{"last_name":"Veldhorst","first_name":"Menno","full_name":"Veldhorst, Menno"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"_id":"8831","external_id":{"arxiv":["2012.00322"]},"department":[{"_id":"GeKa"}],"acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_processing_charge":"No","citation":{"ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. <i>arXiv</i>.","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” <i>ArXiv</i>, n.d.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.).","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. <i>arXiv</i>.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” <i>ArXiv</i>, 2012.00322.","ieee":"K. Aggarwal <i>et al.</i>, “Enhancement of proximity induced superconductivity in planar Germanium,” <i>arXiv</i>. .","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322."},"status":"public","type":"preprint","title":"Enhancement of proximity induced superconductivity in planar Germanium","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"10559"},{"status":"public","relation":"research_data","id":"8834"},{"relation":"dissertation_contains","id":"10058","status":"public"}]},"month":"12","oa_version":"Submitted Version","ddc":["530"],"date_updated":"2024-03-25T23:30:14Z","publication_status":"submitted","oa":1,"arxiv":1,"has_accepted_license":"1","article_number":"2012.00322"},{"date_created":"2020-12-02T10:49:30Z","doi":"10.15479/AT:ISTA:8834","_id":"8834","contributor":[{"id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","contributor_type":"project_member","first_name":"Kushagra","last_name":"Aggarwal"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea 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Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>","chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>.","short":"G. Katsaros, (2020).","ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>."},"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Enhancement of proximity induced superconductivity in planar Germanium","type":"research_data","status":"public","oa_version":"Published Version","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"10559","relation":"used_in_publication","status":"public"},{"status":"public","id":"8831","relation":"used_in_publication"}]},"day":"02","year":"2020","oa":1,"ddc":["530"],"date_updated":"2024-02-21T12:41:26Z","has_accepted_license":"1","file_date_updated":"2020-12-02T10:46:27Z","author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"}],"abstract":[{"text":"This data collection contains the transport data for figures presented in the supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n","lang":"eng"}],"date_published":"2020-12-02T00:00:00Z"}]