[{"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","volume":169,"type":"book_chapter","ddc":["573"],"intvolume":"       169","alternative_title":["Neuromethods"],"language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-1-0716-1522-5_19","date_published":"2021-07-27T00:00:00Z","place":"New York","acknowledgement":"This work was supported by the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.) and the Austrian Academy of Sciences (DOC fellowship to D.K.).","page":"267-283","publisher":"Humana","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"month":"07","publication_identifier":{"eisbn":["9781071615225"],"isbn":["9781071615218"]},"publication":" Receptor and Ion Channel Detection in the Brain","day":"27","citation":{"short":"W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:,  Receptor and Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.","chicago":"Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i> Receptor and Ion Channel Detection in the Brain</i>, 169:267–83. Neuromethods. New York: Humana, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>.","ista":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In:  Receptor and Ion Channel Detection in the Brain. Neuromethods, vol. 169, 267–283.","mla":"Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i> Receptor and Ion Channel Detection in the Brain</i>, vol. 169, Humana, 2021, pp. 267–83, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>.","ieee":"W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL),” in <i> Receptor and Ion Channel Detection in the Brain</i>, vol. 169, New York: Humana, 2021, pp. 267–283.","ama":"Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In: <i> Receptor and Ion Channel Detection in the Brain</i>. Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">10.1007/978-1-0716-1522-5_19</a>","apa":"Kaufmann, W., Kleindienst, D., Harada, H., &#38; Shigemoto, R. (2021). High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL). In <i> Receptor and Ion Channel Detection in the Brain</i> (Vol. 169, pp. 267–283). New York: Humana. <a href=\"https://doi.org/10.1007/978-1-0716-1522-5_19\">https://doi.org/10.1007/978-1-0716-1522-5_19</a>"},"date_updated":"2024-03-25T23:30:16Z","author":[{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"},{"full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","first_name":"Harumi","last_name":"Harada"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"has_accepted_license":"1","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"title":"High-Resolution localization and quantitation of membrane proteins by SDS-digested freeze-fracture replica labeling (SDS-FRL)","year":"2021","_id":"9756","ec_funded":1,"date_created":"2021-07-30T09:34:56Z","series_title":"Neuromethods","oa_version":"None","article_processing_charge":"No","keyword":["Freeze-fracture replica: Deep learning","Immunogold labeling","Integral membrane protein","Electron microscopy"],"quality_controlled":"1","abstract":[{"lang":"eng","text":"High-resolution visualization and quantification of membrane proteins contribute to the understanding of their functions and the roles they play in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively the two-dimensional distribution of transmembrane proteins and their tightly associated proteins. During treatment with SDS, intracellular organelles and proteins not anchored to the replica are dissolved, whereas integral membrane proteins captured and stabilized by carbon/platinum deposition remain on the replica. Their intra- and extracellular domains become exposed on the surface of the replica, facilitating the accessibility of antibodies and, therefore, providing higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples, and optimization of the SDS treatment to increase the labeling efficiency for quantification of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing deep learning algorithms."}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9562"}]}},{"external_id":{"isi":["000677713500008"],"pmid":["34264932"]},"title":"Ten simple rules to improve academic work- life balance","issue":"7","article_number":"e1009124","has_accepted_license":"1","citation":{"chicago":"Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>.","ista":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124.","mla":"Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” <i>PLoS Computational Biology</i>, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>.","apa":"Bartlett, M. J., Arslan, F. N., Bankston, A., &#38; Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">https://doi.org/10.1371/journal.pcbi.1009124</a>","ieee":"M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” <i>PLoS Computational Biology</i>, vol. 17, no. 7. Public Library of Science, 2021.","ama":"Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. <i>PLoS Computational Biology</i>. 2021;17(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009124\">10.1371/journal.pcbi.1009124</a>","short":"M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021)."},"author":[{"full_name":"Bartlett, Michael John","last_name":"Bartlett","first_name":"Michael John"},{"full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","first_name":"Feyza N","last_name":"Arslan"},{"full_name":"Bankston, Adriana","last_name":"Bankston","first_name":"Adriana"},{"full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz","last_name":"Sarabipour"}],"date_updated":"2023-08-10T14:16:46Z","publication":"PLoS Computational Biology","publication_identifier":{"eissn":["15537358"],"issn":["1553734X"]},"oa":1,"day":"15","file":[{"access_level":"open_access","creator":"cchlebak","file_size":693633,"content_type":"application/pdf","checksum":"e56d91f0eeadb36f143a90e2c1b3ab63","date_updated":"2021-08-05T12:06:49Z","file_id":"9771","relation":"main_file","date_created":"2021-08-05T12:06:49Z","file_name":"2021_PlosCompBio_Bartlett.pdf"}],"article_type":"letter_note","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes","year":"2021","_id":"9759","date_created":"2021-08-01T22:01:21Z","pmid":1,"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1371/journal.pcbi.1009124","date_published":"2021-07-15T00:00:00Z","ddc":["613"],"intvolume":"        17","volume":17,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-08-05T12:06:49Z","department":[{"_id":"CaHe"}],"publisher":"Public Library of Science","month":"07","isi":1,"scopus_import":"1","acknowledgement":"The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program."},{"isi":1,"month":"07","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","scopus_import":"1","arxiv":1,"intvolume":"         5","ddc":["530"],"date_published":"2021-07-01T00:00:00Z","doi":"10.22331/Q-2021-07-01-491","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2021-08-06T06:44:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":5,"quality_controlled":"1","article_processing_charge":"Yes","oa_version":"Published Version","publication_status":"published","article_type":"original","related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.","lang":"eng"}],"file":[{"access_level":"open_access","creator":"cchlebak","checksum":"9706c2bb8e748e9b5b138381995a7f6f","content_type":"application/pdf","file_size":2312482,"date_updated":"2021-08-06T06:44:31Z","file_name":"2021_Quantum_Sack.pdf","file_id":"9774","relation":"main_file","date_created":"2021-08-06T06:44:31Z"}],"date_created":"2021-08-01T22:01:21Z","ec_funded":1,"_id":"9760","year":"2021","has_accepted_license":"1","article_number":"491","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"day":"01","oa":1,"publication":"Quantum","publication_identifier":{"eissn":["2521-327X"]},"author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","last_name":"Sack","first_name":"Stefan"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn"}],"citation":{"mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>.","apa":"Sack, S., &#38; Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>","ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. 2021;5. doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” <i>Quantum</i>, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>.","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","short":"S. Sack, M. Serbyn, Quantum 5 (2021)."},"date_updated":"2023-12-13T14:47:25Z"},{"acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","scopus_import":"1","isi":1,"month":"06","publisher":"MDPI","department":[{"_id":"SaSi"}],"file_date_updated":"2021-08-04T14:01:30Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":10,"ddc":["570"],"intvolume":"        10","date_published":"2021-06-25T00:00:00Z","doi":"10.3390/cells10071593","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"pmid":1,"date_created":"2021-08-01T22:01:22Z","_id":"9761","year":"2021","quality_controlled":"1","article_processing_charge":"Yes","oa_version":"Published Version","article_type":"original","publication_status":"published","abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}],"file":[{"access_level":"open_access","creator":"cziletti","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","content_type":"application/pdf","file_size":4555611,"date_updated":"2021-08-04T14:01:30Z","file_name":"2021_Cells_Muench.pdf","file_id":"9768","success":1,"date_created":"2021-08-04T14:01:30Z","relation":"main_file"}],"day":"25","oa":1,"publication_identifier":{"eissn":["20734409"]},"publication":"Cells","author":[{"full_name":"Muench, Nicole A.","first_name":"Nicole A.","last_name":"Muench"},{"full_name":"Patel, Sonia","first_name":"Sonia","last_name":"Patel"},{"orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","first_name":"Margaret E"},{"full_name":"Donahue, Ryan J.","last_name":"Donahue","first_name":"Ryan J."},{"full_name":"Ikeda, Akihiro","first_name":"Akihiro","last_name":"Ikeda"},{"full_name":"Nickells, Robert W.","last_name":"Nickells","first_name":"Robert W."}],"citation":{"short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., &#38; Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” <i>Cells</i>, vol. 10, no. 7. MDPI, 2021.","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. 2021;10(7). doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>, vol. 10, no. 7, 1593, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>."},"date_updated":"2023-08-10T14:14:53Z","has_accepted_license":"1","article_number":"1593","issue":"7","external_id":{"pmid":["34201955"],"isi":["000678193300001"]},"title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease"},{"intvolume":"        11","ddc":["530"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"date_published":"2021-07-13T00:00:00Z","doi":"10.21468/scipostphys.11.1.008","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-08-10T11:44:59Z","volume":11,"type":"journal_article","isi":1,"month":"07","publisher":"SciPost","department":[{"_id":"MiLe"}],"scopus_import":"1","acknowledgement":"We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks\". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245.","arxiv":1,"article_number":"008","issue":"1","has_accepted_license":"1","title":"Impurities in a one-dimensional Bose gas: The flow equation approach","external_id":{"isi":["000680039500013"],"arxiv":["2101.10958"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020"}],"oa":1,"publication_identifier":{"eissn":["2542-4653"]},"publication":"SciPost Physics","day":"13","citation":{"chicago":"Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>. SciPost, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>.","ista":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.","mla":"Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” <i>SciPost Physics</i>, vol. 11, no. 1, 008, SciPost, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>.","ieee":"F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” <i>SciPost Physics</i>, vol. 11, no. 1. SciPost, 2021.","ama":"Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">10.21468/scipostphys.11.1.008</a>","apa":"Brauneis, F., Hammer, H.-W., Lemeshko, M., &#38; Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. <i>SciPost Physics</i>. SciPost. <a href=\"https://doi.org/10.21468/scipostphys.11.1.008\">https://doi.org/10.21468/scipostphys.11.1.008</a>","short":"F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021)."},"author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"full_name":"Hammer, Hans-Werner","last_name":"Hammer","first_name":"Hans-Werner"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-11T10:25:44Z","article_processing_charge":"Yes","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak."}],"file":[{"creator":"asandaue","access_level":"open_access","checksum":"eaa847346b1a023d97bbb291779610ed","file_size":1085300,"content_type":"application/pdf","date_updated":"2021-08-10T11:44:59Z","file_name":"2021_SciPostPhysics_Brauneis.pdf","date_created":"2021-08-10T11:44:59Z","relation":"main_file","success":1,"file_id":"9875"}],"article_type":"original","publication_status":"published","_id":"9769","year":"2021","date_created":"2021-08-04T15:00:55Z","ec_funded":1},{"scopus_import":"1","acknowledgement":"We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science.","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/2101.05173","open_access":"1"}],"isi":1,"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":104,"type":"journal_article","intvolume":"       104","language":[{"iso":"eng"}],"status":"public","doi":"10.1103/physrevb.104.024430","date_published":"2021-07-01T00:00:00Z","year":"2021","_id":"9770","date_created":"2021-08-04T15:05:32Z","ec_funded":1,"oa_version":"Preprint","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data.","lang":"eng"}],"article_type":"original","publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication":"Physical Review B","oa":1,"day":"01","author":[{"first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"},{"first_name":"Hen","last_name":"Alpern","full_name":"Alpern, Hen"},{"first_name":"Yossi","last_name":"Paltiel","full_name":"Paltiel, Yossi"},{"last_name":"Millo","first_name":"Oded","full_name":"Millo, Oded"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"},{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan"}],"citation":{"short":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021).","mla":"Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>.","ama":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. 2021;104(2). doi:<a href=\"https://doi.org/10.1103/physrevb.104.024430\">10.1103/physrevb.104.024430</a>","ieee":"A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” <i>Physical Review B</i>, vol. 104, no. 2. American Physical Society, 2021.","apa":"Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., &#38; Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>","chicago":"Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevb.104.024430\">https://doi.org/10.1103/physrevb.104.024430</a>.","ista":"Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430."},"date_updated":"2023-08-10T14:27:07Z","issue":"2","article_number":"024430","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"external_id":{"isi":["000678780800003"],"arxiv":["2101.05173"]},"title":"Interplay between friction and spin-orbit coupling as a source of spin polarization"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-12-17T11:34:50Z","volume":12,"type":"journal_article","intvolume":"        12","ddc":["570"],"language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1038/s41467-021-23153-5","date_published":"2021-05-18T00:00:00Z","scopus_import":"1","acknowledgement":"We thank Drs. Carolina Borges-Merjane and Jose Guzman for critically reading the manuscript, and Pablo Castillo for discussions. We are grateful to Alois Schlögl for help with analysis, Florian Marr for excellent technical assistance and cell reconstruction, Christina Altmutter for technical help, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for support. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 692692) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award), both to P.J.","isi":1,"department":[{"_id":"PeJo"}],"publisher":"Springer","month":"05","publication_identifier":{"issn":["2041-1723"]},"publication":"Nature Communications","oa":1,"day":"18","citation":{"short":"D.H. Vandael, Y. Okamoto, P.M. Jonas, Nature Communications 12 (2021).","mla":"Vandael, David H., et al. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>, vol. 12, no. 1, 2912, Springer, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>.","apa":"Vandael, D. H., Okamoto, Y., &#38; Jonas, P. M. (2021). Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. Springer. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>","ieee":"D. H. Vandael, Y. Okamoto, and P. M. Jonas, “Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses,” <i>Nature Communications</i>, vol. 12, no. 1. Springer, 2021.","ama":"Vandael DH, Okamoto Y, Jonas PM. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23153-5\">10.1038/s41467-021-23153-5</a>","chicago":"Vandael, David H, Yuji Okamoto, and Peter M Jonas. “Transsynaptic Modulation of Presynaptic Short-Term Plasticity in Hippocampal Mossy Fiber Synapses.” <i>Nature Communications</i>. Springer, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23153-5\">https://doi.org/10.1038/s41467-021-23153-5</a>.","ista":"Vandael DH, Okamoto Y, Jonas PM. 2021. Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses. Nature Communications. 12(1), 2912."},"date_updated":"2023-08-10T14:16:16Z","author":[{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H"},{"last_name":"Okamoto","first_name":"Yuji","full_name":"Okamoto, Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"article_number":"2912","issue":"1","has_accepted_license":"1","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000655481800014"]},"title":"Transsynaptic modulation of presynaptic short-term plasticity in hippocampal mossy fiber synapses","year":"2021","_id":"9778","date_created":"2021-08-06T07:22:55Z","ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","article_processing_charge":"No","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"quality_controlled":"1","file":[{"access_level":"open_access","creator":"kschuh","checksum":"6036a8cdae95e1707c2a04d54e325ff4","content_type":"application/pdf","file_size":3108845,"date_updated":"2021-12-17T11:34:50Z","file_name":"2021_NatureCommunications_Vandael.pdf","file_id":"10563","relation":"main_file","date_created":"2021-12-17T11:34:50Z","success":1}],"abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse is a key synapse of the trisynaptic circuit. Post-tetanic potentiation (PTP) is the most powerful form of plasticity at this synaptic connection. It is widely believed that mossy fiber PTP is an entirely presynaptic phenomenon, implying that PTP induction is input-specific, and requires neither activity of multiple inputs nor stimulation of postsynaptic neurons. To directly test cooperativity and associativity, we made paired recordings between single mossy fiber terminals and postsynaptic CA3 pyramidal neurons in rat brain slices. By stimulating non-overlapping mossy fiber inputs converging onto single CA3 neurons, we confirm that PTP is input-specific and non-cooperative. Unexpectedly, mossy fiber PTP exhibits anti-associative induction properties. EPSCs show only minimal PTP after combined pre- and postsynaptic high-frequency stimulation with intact postsynaptic Ca2+ signaling, but marked PTP in the absence of postsynaptic spiking and after suppression of postsynaptic Ca2+ signaling (10 mM EGTA). PTP is largely recovered by inhibitors of voltage-gated R- and L-type Ca2+ channels, group II mGluRs, and vacuolar-type H+-ATPase, suggesting the involvement of retrograde vesicular glutamate signaling. Transsynaptic regulation of PTP extends the repertoire of synaptic computations, implementing a brake on mossy fiber detonation and a “smart teacher” function of hippocampal mossy fiber synapses."}],"publication_status":"published","article_type":"original","related_material":{"link":[{"url":"https://ist.ac.at/en/news/synaptic-transmission-not-a-one-way-street/","description":"News on IST Homepage","relation":"press_release"}]}},{"department":[{"_id":"RoSe"}],"month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.12566"}],"arxiv":1,"acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.1.\r\n","date_published":"2021-02-01T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","ddc":["510"],"type":"preprint","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","related_material":{"record":[{"id":"10224","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"9733"}]},"publication_status":"submitted","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","ec_funded":1,"date_created":"2021-08-06T08:25:57Z","year":"2021","_id":"9787","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"}],"external_id":{"arxiv":["2101.12566"]},"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","has_accepted_license":"1","article_number":"2101.12566","citation":{"short":"D. Feliciangeli, R. Seiringer, ArXiv (n.d.).","ista":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. arXiv, 2101.12566.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>ArXiv</i>, n.d.","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” <i>arXiv</i>. .","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>arXiv</i>.","apa":"Feliciangeli, D., &#38; Seiringer, R. (n.d.). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>arXiv</i>.","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>ArXiv</i>, 2101.12566."},"author":[{"first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T13:30:10Z","day":"01","publication":"arXiv","oa":1},{"oa":1,"publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","type":"preprint","author":[{"full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","last_name":"Feliciangeli"},{"full_name":"Rademacher, Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","orcid":"0000-0001-5059-4466","first_name":"Simone Anna Elvira","last_name":"Rademacher"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"citation":{"mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>ArXiv</i>, 2107.03720.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. <i>arXiv</i>.","apa":"Feliciangeli, D., Rademacher, S. A. E., &#38; Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. <i>arXiv</i>.","ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” <i>arXiv</i>. .","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>ArXiv</i>, n.d.","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.)."},"date_updated":"2024-03-06T12:30:45Z","ddc":["510"],"article_number":"2107.03720 ","title":"The effective mass problem for the Landau-Pekar equations","external_id":{"arxiv":["2107.03720"]},"status":"public","language":[{"iso":"eng"}],"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"}],"date_published":"2021-07-08T00:00:00Z","_id":"9791","year":"2021","acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","date_created":"2021-08-06T08:49:45Z","ec_funded":1,"arxiv":1,"article_processing_charge":"No","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.03720"}],"abstract":[{"lang":"eng","text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar."}],"month":"07","publication_status":"submitted","department":[{"_id":"RoSe"}],"related_material":{"record":[{"status":"public","id":"10755","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"9733"}]}},{"citation":{"ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” <i>arXiv</i>. .","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2106.11217\">10.48550/arXiv.2106.11217</a>","apa":"Feliciangeli, D., Gerolin, A., &#38; Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2106.11217\">https://doi.org/10.48550/arXiv.2106.11217</a>","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>ArXiv</i>, 2106.11217, doi:<a href=\"https://doi.org/10.48550/arXiv.2106.11217\">10.48550/arXiv.2106.11217</a>.","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2106.11217\">https://doi.org/10.48550/arXiv.2106.11217</a>.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.)."},"author":[{"last_name":"Feliciangeli","first_name":"Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"},{"first_name":"Augusto","last_name":"Gerolin","full_name":"Gerolin, Augusto"},{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"}],"date_updated":"2023-11-14T13:21:01Z","publication":"arXiv","oa":1,"day":"21","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"external_id":{"arxiv":["2106.11217"]},"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","article_number":"2106.11217","has_accepted_license":"1","year":"2021","_id":"9792","date_created":"2021-08-06T09:07:12Z","ec_funded":1,"abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"related_material":{"record":[{"id":"9733","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"10030"},{"relation":"later_version","id":"12911","status":"public"}]},"publication_status":"submitted","oa_version":"Preprint","article_processing_charge":"No","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.48550/arXiv.2106.11217","date_published":"2021-07-21T00:00:00Z","ddc":["510"],"arxiv":1,"acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article.  L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"month":"07","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}]},{"publisher":"Elsevier","department":[{"_id":"SiHi"}],"month":"08","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2021.05.025","open_access":"1"}],"isi":1,"page":"2427-2442.e10","scopus_import":"1","acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","language":[{"iso":"eng"}],"status":"public","doi":"10.1016/j.neuron.2021.05.025","date_published":"2021-08-04T00:00:00Z","intvolume":"       109","volume":109,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology.","lang":"eng"}],"article_type":"original","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","quality_controlled":"1","year":"2021","_id":"9793","pmid":1,"date_created":"2021-08-06T09:08:25Z","ec_funded":1,"project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"HepaCAM controls astrocyte self-organization and coupling","external_id":{"isi":["000692851900010"],"pmid":["34171291"]},"issue":"15","citation":{"short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10.","ieee":"K. T. Baldwin <i>et al.</i>, “HepaCAM controls astrocyte self-organization and coupling,” <i>Neuron</i>, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021.","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. 2021;109(15):2427-2442.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>","mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>.","ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.","chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>."},"author":[{"first_name":"Katherine T.","last_name":"Baldwin","full_name":"Baldwin, Katherine T."},{"full_name":"Tan, Christabel X.","first_name":"Christabel X.","last_name":"Tan"},{"full_name":"Strader, Samuel T.","last_name":"Strader","first_name":"Samuel T."},{"full_name":"Jiang, Changyu","last_name":"Jiang","first_name":"Changyu"},{"full_name":"Savage, Justin T.","last_name":"Savage","first_name":"Justin T."},{"full_name":"Elorza-Vidal, Xabier","last_name":"Elorza-Vidal","first_name":"Xabier"},{"first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Estévez, Raúl","last_name":"Estévez","first_name":"Raúl"},{"full_name":"Ji, Ru-Rong","last_name":"Ji","first_name":"Ru-Rong"},{"full_name":"Eroglu, Cagla","first_name":"Cagla","last_name":"Eroglu"}],"date_updated":"2023-09-27T07:46:09Z","publication":"Neuron","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"oa":1,"day":"04"},{"scopus_import":"1","acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","arxiv":1,"isi":1,"department":[{"_id":"JoFi"}],"publisher":"IOP Publishing","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-08-09T12:23:13Z","volume":6,"type":"journal_article","intvolume":"         6","ddc":["530"],"language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1088/2058-9565/ac0f36","date_published":"2021-07-15T00:00:00Z","year":"2021","_id":"9815","date_created":"2021-08-08T22:01:25Z","oa_version":"Published Version","article_processing_charge":"Yes","quality_controlled":"1","file":[{"date_updated":"2021-08-09T12:23:13Z","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","relation":"main_file","date_created":"2021-08-09T12:23:13Z","file_id":"9836","creator":"cchlebak","access_level":"open_access","checksum":"b15c2c228487a75002c3b52d56f23d5c","content_type":"application/pdf","file_size":2366118}],"abstract":[{"lang":"eng","text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion."}],"article_type":"original","publication_status":"published","publication":"Quantum Science and Technology","publication_identifier":{"eissn":["2058-9565"]},"oa":1,"day":"15","date_updated":"2023-10-17T12:54:54Z","author":[{"full_name":"Mobassem, Sonia","first_name":"Sonia","last_name":"Mobassem"},{"first_name":"Nicholas J.","last_name":"Lambert","full_name":"Lambert, Nicholas J."},{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"citation":{"chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>.","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005.","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>.","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. 2021;6(4). doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>","ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” <i>Quantum Science and Technology</i>, vol. 6, no. 4. IOP Publishing, 2021.","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., &#38; Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021)."},"issue":"4","article_number":"045005","has_accepted_license":"1","title":"Thermal noise in electro-optic devices at cryogenic temperatures","external_id":{"arxiv":["2008.08764"],"isi":["000673081500001"]}},{"citation":{"mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>.","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &#38; Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021)."},"date_updated":"2023-08-10T14:26:32Z","author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mathias","last_name":"Beiglböck","full_name":"Beiglböck, Mathias"},{"last_name":"Herdina","first_name":"Anna Nele","full_name":"Herdina, Anna Nele"},{"last_name":"Strassl","first_name":"Robert","full_name":"Strassl, Robert"},{"full_name":"Posch, Martin","first_name":"Martin","last_name":"Posch"}],"publication":"PLoS ONE","publication_identifier":{"eissn":["1932-6203"]},"oa":1,"day":"29","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","external_id":{"pmid":["34324553"],"isi":["000685248200095"]},"article_number":"e0255267","issue":"7","has_accepted_license":"1","year":"2021","_id":"9816","date_created":"2021-08-08T22:01:26Z","pmid":1,"file":[{"date_updated":"2021-08-09T11:52:14Z","file_name":"2021_PLoSONE_Hledík.pdf","relation":"main_file","date_created":"2021-08-09T11:52:14Z","success":1,"file_id":"9835","creator":"asandaue","access_level":"open_access","checksum":"ae4df60eb62f4491278588548d0c1f93","content_type":"application/pdf","file_size":773921}],"abstract":[{"text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test.","lang":"eng"}],"publication_status":"published","article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes","quality_controlled":"1","volume":16,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-08-09T11:52:14Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1371/journal.pone.0255267","date_published":"2021-07-29T00:00:00Z","intvolume":"        16","ddc":["610"],"scopus_import":"1","acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"month":"07","isi":1},{"abstract":[{"lang":"eng","text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements."}],"file":[{"success":1,"date_created":"2021-10-18T10:42:15Z","relation":"main_file","file_id":"10150","file_name":"elastic-curves-paper.pdf","date_updated":"2021-10-18T10:42:15Z","content_type":"application/pdf","file_size":17064290,"checksum":"7e5d08ce46b0451b3102eacd3d00f85f","creator":"chafner","access_level":"open_access"},{"access_level":"open_access","creator":"chafner","checksum":"0088643478be7c01a703b5b10767348f","content_type":"application/pdf","file_size":547156,"date_updated":"2021-10-18T10:42:22Z","file_name":"elastic-curves-supp.pdf","file_id":"10151","relation":"supplementary_material","date_created":"2021-10-18T10:42:22Z"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"12897","status":"public"}],"link":[{"relation":"press_release","description":"News on IST Website","url":"https://ist.ac.at/en/news/designing-with-elastic-structures/"}]},"article_type":"original","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","_id":"9817","year":"2021","ec_funded":1,"date_created":"2021-08-08T22:01:26Z","title":"The design space of plane elastic curves","external_id":{"isi":["000674930900091"]},"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"article_number":"126","issue":"4","has_accepted_license":"1","date_updated":"2024-03-25T23:30:26Z","citation":{"ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>","apa":"Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126.","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021)."},"author":[{"full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","first_name":"Christian"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"}],"oa":1,"publication":"ACM Transactions on Graphics","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"day":"19","month":"07","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"isi":1,"conference":{"end_date":"2021-08-13","name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Virtual","start_date":"2021-08-09"},"scopus_import":"1","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"date_published":"2021-07-19T00:00:00Z","doi":"10.1145/3450626.3459800","ddc":["516"],"intvolume":"        40","volume":40,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-10-18T10:42:22Z"},{"date_updated":"2023-08-10T14:24:36Z","citation":{"short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168."},"author":[{"first_name":"Georg","last_name":"Sperl","full_name":"Sperl, Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Narain","first_name":"Rahul","full_name":"Narain, Rahul"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J"}],"oa":1,"publication":"ACM Transactions on Graphics","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"day":"01","title":"Mechanics-aware deformation of yarn pattern geometry","external_id":{"isi":["000674930900132"]},"project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"issue":"4","article_number":"168","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"9818","year":"2021","date_created":"2021-08-08T22:01:27Z","ec_funded":1,"abstract":[{"text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.","lang":"eng"}],"article_type":"original","related_material":{"record":[{"status":"public","id":"12358","relation":"dissertation_contains"},{"status":"public","id":"9327","relation":"software"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/","description":"News on IST Webpage"}]},"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","quality_controlled":"1","volume":40,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","language":[{"iso":"eng"}],"date_published":"2021-08-01T00:00:00Z","doi":"10.1145/3450626.3459816","intvolume":"        40","scopus_import":"1","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","month":"08","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"isi":1},{"ddc":["000"],"intvolume":"        40","doi":"10.1145/3450626.3459765","date_published":"2021-08-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2021-08-09T11:41:50Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":40,"isi":1,"department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","month":"08","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","scopus_import":"1","arxiv":1,"has_accepted_license":"1","article_number":"44","issue":"4","title":"PhotoApp: Photorealistic appearance editing of head portraits","external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"day":"01","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"publication":"ACM Transactions on Graphics","oa":1,"citation":{"short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021).","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>","ieee":"B. R. Mallikarjun <i>et al.</i>, “PhotoApp: Photorealistic appearance editing of head portraits,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>.","ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>."},"date_updated":"2023-08-10T14:25:08Z","author":[{"last_name":"Mallikarjun","first_name":"B. R.","full_name":"Mallikarjun, B. R."},{"first_name":"Ayush","last_name":"Tewari","full_name":"Tewari, Ayush"},{"last_name":"Dib","first_name":"Abdallah","full_name":"Dib, Abdallah"},{"last_name":"Weyrich","first_name":"Tim","full_name":"Weyrich, Tim"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"full_name":"Chevallier, Louis","last_name":"Chevallier","first_name":"Louis"},{"full_name":"Elgharib, Mohamed A.","last_name":"Elgharib","first_name":"Mohamed A."},{"full_name":"Theobalt, Christian","first_name":"Christian","last_name":"Theobalt"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","article_type":"original","file":[{"creator":"asandaue","access_level":"open_access","file_size":49840741,"content_type":"application/pdf","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","date_updated":"2021-08-09T11:41:50Z","date_created":"2021-08-09T11:41:50Z","success":1,"relation":"main_file","file_id":"9834","file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf"}],"abstract":[{"text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates.","lang":"eng"}],"date_created":"2021-08-08T22:01:27Z","year":"2021","_id":"9819"},{"publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"month":"08","main_file_link":[{"open_access":"1","url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf"}],"isi":1,"scopus_import":"1","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","language":[{"iso":"eng"}],"status":"public","doi":"10.1145/3450626.3459813","date_published":"2021-08-01T00:00:00Z","intvolume":"        40","volume":40,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design.","lang":"eng"}],"article_type":"original","publication_status":"published","oa_version":"Submitted Version","article_processing_charge":"No","quality_controlled":"1","year":"2021","_id":"9820","date_created":"2021-08-08T22:01:28Z","title":"The effect of shape and illumination on material perception: Model and applications","external_id":{"isi":["000674930900090"]},"article_number":"125","issue":"4","date_updated":"2023-08-10T14:20:10Z","author":[{"full_name":"Serrano, Ana","first_name":"Ana","last_name":"Serrano"},{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"full_name":"Wang, Chao","first_name":"Chao","last_name":"Wang"},{"first_name":"Michael","last_name":"Piovarci","orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E"},{"first_name":"Hans Peter","last_name":"Seidel","full_name":"Seidel, Hans Peter"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"}],"citation":{"ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>","ieee":"A. Serrano <i>et al.</i>, “The effect of shape and illumination on material perception: Model and applications,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &#38; Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>.","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.","chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021)."},"publication":"ACM Transactions on Graphics","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"oa":1,"day":"01"},{"type":"journal_article","volume":16,"file_date_updated":"2021-08-09T09:25:41Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-07-01T00:00:00Z","doi":"10.1371/journal.pone.0253851","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"intvolume":"        16","ddc":["006"],"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","scopus_import":"1","month":"07","publisher":"Public Library of Science","department":[{"_id":"HeEd"}],"isi":1,"author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","first_name":"Beata","last_name":"Graff"},{"last_name":"Pilarczyk","first_name":"Pawel","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jablonski, Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","first_name":"Grzegorz","last_name":"Jablonski"},{"full_name":"Gąsecki, Dariusz","last_name":"Gąsecki","first_name":"Dariusz"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"citation":{"mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>.","ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>.","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021)."},"date_updated":"2023-08-10T14:21:42Z","day":"01","oa":1,"publication":"PLoS ONE","publication_identifier":{"eissn":["19326203"]},"title":"Persistent homology as a new method of the assessment of heart rate variability","external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"has_accepted_license":"1","issue":"7","article_number":"e0253851","pmid":1,"date_created":"2021-08-08T22:01:28Z","_id":"9821","year":"2021","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode."}],"file":[{"access_level":"open_access","creator":"asandaue","checksum":"0277aa155d5db1febd2cb384768bba5f","file_size":2706919,"content_type":"application/pdf","date_updated":"2021-08-09T09:25:41Z","file_name":"2021_PLoSONE_Graff.pdf","file_id":"9832","success":1,"date_created":"2021-08-09T09:25:41Z","relation":"main_file"}],"quality_controlled":"1","article_processing_charge":"Yes","oa_version":"Published Version"},{"file":[{"date_updated":"2021-08-09T09:44:03Z","file_id":"9833","date_created":"2021-08-09T09:44:03Z","relation":"main_file","success":1,"file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","access_level":"open_access","creator":"asandaue","file_size":7123293,"content_type":"application/pdf","checksum":"b043a91d9f9200e467b970b692687ed3"}],"abstract":[{"lang":"eng","text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science."}],"article_type":"original","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","year":"2021","_id":"9822","pmid":1,"ec_funded":1,"date_created":"2021-08-08T22:01:28Z","project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","issue":"30","has_accepted_license":"1","author":[{"last_name":"Zisis","first_name":"Themistoklis","full_name":"Zisis, Themistoklis"},{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan"},{"first_name":"Miriam","last_name":"Balles","full_name":"Balles, Miriam"},{"full_name":"Kretschmer, Maibritt","first_name":"Maibritt","last_name":"Kretschmer"},{"last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria"},{"last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"last_name":"Lange","first_name":"Janina","full_name":"Lange, Janina"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C"},{"first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"date_updated":"2023-08-10T14:22:48Z","citation":{"short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>","ieee":"T. Zisis <i>et al.</i>, “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. 2021;13(30):35545–35560. doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>"},"publication":"ACS Applied Materials and Interfaces","publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"oa":1,"day":"04","publisher":"American Chemical Society","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"month":"08","isi":1,"page":"35545–35560","scopus_import":"1","acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","doi":"10.1021/acsami.1c09850","date_published":"2021-08-04T00:00:00Z","intvolume":"        13","ddc":["620","570"],"volume":13,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-08-09T09:44:03Z"},{"publisher":"Springer Nature","department":[{"_id":"DaAl"}],"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08949"}],"arxiv":1,"page":"87-105","conference":{"name":"SIROCCO: Structural Information and Communication Complexity","location":"Wrocław, Poland","start_date":"2021-06-28","end_date":"2021-07-01"},"scopus_import":"1","doi":"10.1007/978-3-030-79527-6_6","date_published":"2021-06-20T00:00:00Z","language":[{"iso":"eng"}],"status":"public","alternative_title":["LNCS"],"intvolume":"     12810","type":"conference","volume":12810,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication_status":"published","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a vertex of the graph as input and, if non-faulty, must output a vertex such that\r\nall the outputs are within distance 1 of one another, and\r\n\r\neach output value lies on a shortest path between two input values.\r\n\r\nFrom prior work, it is known that there is no wait-free algorithm among   𝑛≥3  processes for this problem on any cycle of length   𝑐≥4 , by reduction from 2-set agreement (Castañeda et al. 2018).\r\n\r\nIn this work, we investigate the solvability and complexity of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length   𝑐≥4 , via a generalisation of Sperner’s Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a class of graphs that properly contains the class of chordal graphs.","lang":"eng"}],"quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","date_created":"2021-08-08T22:01:29Z","year":"2021","_id":"9823","title":"Wait-free approximate agreement on graphs","external_id":{"arxiv":["2103.08949"]},"date_updated":"2023-02-23T14:09:49Z","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Faith","last_name":"Ellen","full_name":"Ellen, Faith"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki"}],"citation":{"apa":"Alistarh, D.-A., Ellen, F., &#38; Rybicki, J. (2021). Wait-free approximate agreement on graphs. In <i>Structural Information and Communication Complexity</i> (Vol. 12810, pp. 87–105). Wrocław, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">https://doi.org/10.1007/978-3-030-79527-6_6</a>","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” in <i>Structural Information and Communication Complexity</i>, Wrocław, Poland, 2021, vol. 12810, pp. 87–105.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. In: <i>Structural Information and Communication Complexity</i>. Vol 12810. Springer Nature; 2021:87-105. doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">10.1007/978-3-030-79527-6_6</a>","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” <i>Structural Information and Communication Complexity</i>, vol. 12810, Springer Nature, 2021, pp. 87–105, doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">10.1007/978-3-030-79527-6_6</a>.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2021. Wait-free approximate agreement on graphs. Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 12810, 87–105.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” In <i>Structural Information and Communication Complexity</i>, 12810:87–105. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">https://doi.org/10.1007/978-3-030-79527-6_6</a>.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, in:, Structural Information and Communication Complexity, Springer Nature, 2021, pp. 87–105."},"day":"20","publication":"Structural Information and Communication Complexity","publication_identifier":{"issn":["03029743"],"isbn":["9783030795269"],"eissn":["16113349"]},"oa":1}]