[{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","file":[{"file_name":"2019_FrontiersPlant_Alcantara.pdf","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-16T07:58:43Z","file_size":1532505,"creator":"dernst","file_id":"7185","content_type":"application/pdf","access_level":"open_access","checksum":"995aa838aec2064d93550de82b40bbd1","relation":"main_file"}],"author":[{"full_name":"Alcântara, André","last_name":"Alcântara","first_name":"André"},{"full_name":"Bosch, Jason","last_name":"Bosch","first_name":"Jason"},{"full_name":"Nazari, Fahimeh","first_name":"Fahimeh","last_name":"Nazari"},{"full_name":"Hoffmann, Gesa","last_name":"Hoffmann","first_name":"Gesa"},{"full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","orcid":"0000-0003-1286-7368"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"full_name":"Darino, Martin A.","last_name":"Darino","first_name":"Martin A."},{"full_name":"Olukayode, Toluwase","last_name":"Olukayode","first_name":"Toluwase"},{"first_name":"Daniel","last_name":"Reumann","full_name":"Reumann, Daniel"},{"full_name":"Baggaley, Laura","last_name":"Baggaley","first_name":"Laura"},{"full_name":"Djamei, Armin","first_name":"Armin","last_name":"Djamei"}],"title":"Systematic Y2H screening reveals extensive effector-complex formation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Frontiers","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","_id":"7182","type":"journal_article","file_date_updated":"2020-07-14T12:47:52Z","abstract":[{"text":"During infection pathogens secrete small molecules, termed effectors, to manipulate and control the interaction with their specific hosts. Both the pathogen and the plant are under high selective pressure to rapidly adapt and co-evolve in what is usually referred to as molecular arms race. Components of the host’s immune system form a network that processes information about molecules with a foreign origin and damage-associated signals, integrating them with developmental and abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction networks have been extensively characterized. However, little is known on whether pathogenic effectors form complexes to overcome plant immunity and promote disease. Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces effectors that target hubs in the immune network of the host cell. Here we assess the capability of U. maydis effector candidates to interact with each other, which may play a crucial role during the infection process. Using a systematic yeast-two-hybrid approach and based on a preliminary pooled screen, we selected 63 putative effectors for one-on-one matings with a library of nearly 300 effector candidates. We found that 126 of these effector candidates interacted either with themselves or other predicted effectors. Although the functional relevance of the observed interactions remains elusive, we propose that the observed abundance in complex formation between effectors adds an additional level of complexity to effector research and should be taken into consideration when studying effector evolution and function. Based on this fundamental finding, we suggest various scenarios which could evolutionarily drive the formation and stabilization of an effector interactome.","lang":"eng"}],"scopus_import":"1","citation":{"mla":"Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>, vol. 10, no. 11, 1437, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>.","apa":"Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S., … Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>","chicago":"Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex Formation.” <i>Frontiers in Plant Science</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fpls.2019.01437\">https://doi.org/10.3389/fpls.2019.01437</a>.","short":"A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A. Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science 10 (2019).","ieee":"A. Alcântara <i>et al.</i>, “Systematic Y2H screening reveals extensive effector-complex formation,” <i>Frontiers in Plant Science</i>, vol. 10, no. 11. Frontiers, 2019.","ista":"Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA, Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.","ama":"Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive effector-complex formation. <i>Frontiers in Plant Science</i>. 2019;10(11). doi:<a href=\"https://doi.org/10.3389/fpls.2019.01437\">10.3389/fpls.2019.01437</a>"},"publication_identifier":{"eissn":["1664462X"]},"year":"2019","external_id":{"isi":["000499821700001"],"pmid":["31803201"]},"issue":"11","oa":1,"date_updated":"2023-09-06T14:33:46Z","article_number":"1437","intvolume":"        10","month":"11","date_published":"2019-11-14T00:00:00Z","isi":1,"oa_version":"Published Version","doi":"10.3389/fpls.2019.01437","publication":"Frontiers in Plant Science","day":"14","status":"public","date_created":"2019-12-15T23:00:43Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"pmid":1,"volume":10},{"oa":1,"date_updated":"2023-09-06T12:40:58Z","alternative_title":["LNCS"],"date_published":"2019-10-21T00:00:00Z","intvolume":"     11781","month":"10","year":"2019","conference":{"location":"Taipei, Taiwan","name":"ATVA: Automated TEchnology for Verification and Analysis","end_date":"2019-10-31","start_date":"2019-10-28"},"page":"462-478","external_id":{"arxiv":["1907.11010"],"isi":["000723515700027"]},"day":"21","status":"public","date_created":"2019-12-15T23:00:44Z","volume":11781,"oa_version":"Preprint","isi":1,"publication":"International Symposium on Automated Technology for Verification and Analysis","doi":"10.1007/978-3-030-31784-3_27","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11010"}],"title":"Deciding fast termination for probabilistic VASS with nondeterminism","author":[{"last_name":"Brázdil","first_name":"Tomás","full_name":"Brázdil, Tomás"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Antonín","last_name":"Kucera","full_name":"Kucera, Antonín"},{"full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotný"},{"last_name":"Velan","first_name":"Dominik","full_name":"Velan, Dominik"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"article_processing_charge":"No","quality_controlled":"1","_id":"7183","abstract":[{"lang":"eng","text":"A probabilistic vector addition system with states (pVASS) is a finite state Markov process augmented with non-negative integer counters that can be incremented or decremented during each state transition, blocking any behaviour that would cause a counter to decrease below zero. The pVASS can be used as abstractions of probabilistic programs with many decidable properties. The use of pVASS as abstractions requires the presence of nondeterminism in the model. In this paper, we develop techniques for checking fast termination of pVASS with nondeterminism. That is, for every initial configuration of size n, we consider the worst expected number of transitions needed to reach a configuration with some counter negative (the expected termination time). We show that the problem whether the asymptotic expected termination time is linear is decidable in polynomial time for a certain natural class of pVASS with nondeterminism. Furthermore, we show the following dichotomy: if the asymptotic expected termination time is not linear, then it is at least quadratic, i.e., in Ω(n2)."}],"arxiv":1,"scopus_import":"1","type":"conference","citation":{"chicago":"Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” In <i>International Symposium on Automated Technology for Verification and Analysis</i>, 11781:462–78. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>.","short":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2019, pp. 462–478.","ista":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast termination for probabilistic VASS with nondeterminism. International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology for Verification and Analysis, LNCS, vol. 11781, 462–478.","ieee":"T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding fast termination for probabilistic VASS with nondeterminism,” in <i>International Symposium on Automated Technology for Verification and Analysis</i>, Taipei, Taiwan, 2019, vol. 11781, pp. 462–478.","ama":"Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination for probabilistic VASS with nondeterminism. In: <i>International Symposium on Automated Technology for Verification and Analysis</i>. Vol 11781. Springer Nature; 2019:462-478. doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>","mla":"Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.” <i>International Symposium on Automated Technology for Verification and Analysis</i>, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:<a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">10.1007/978-3-030-31784-3_27</a>.","apa":"Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., &#38; Velan, D. (2019). Deciding fast termination for probabilistic VASS with nondeterminism. In <i>International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 11781, pp. 462–478). Taipei, Taiwan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31784-3_27\">https://doi.org/10.1007/978-3-030-31784-3_27</a>"},"publication_identifier":{"issn":["03029743"],"isbn":["9783030317836"],"eissn":["16113349"]},"publication_status":"published","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}]},{"doi":"10.15479/AT:ISTA:7186","degree_awarded":"PhD","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1096"},{"status":"public","relation":"part_of_dissertation","id":"7001"}]},"status":"public","day":"16","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"date_created":"2019-12-16T14:26:14Z","ddc":["570"],"page":"107","year":"2019","alternative_title":["ISTA Thesis"],"date_published":"2019-12-16T00:00:00Z","month":"12","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"oa":1,"date_updated":"2023-09-07T12:56:42Z","publication_status":"published","abstract":[{"text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:52Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"citation":{"apa":"Schwayer, C. (2019). <i>Mechanosensation of tight junctions depends on ZO-1 phase separation and flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>","mla":"Schwayer, Cornelia. <i>Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>.","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>."},"_id":"7186","department":[{"_id":"CaHe"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","author":[{"last_name":"Schwayer","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","full_name":"Schwayer, Cornelia"}],"file":[{"file_name":"DocumentSourceFiles.zip","date_created":"2019-12-19T15:18:11Z","date_updated":"2020-07-14T12:47:52Z","content_type":"application/zip","file_id":"7194","file_size":19431292,"creator":"cschwayer","relation":"source_file","checksum":"585583c1c875c5d9525703a539668a7c","access_level":"closed"},{"date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-19T15:19:21Z","file_name":"Thesis_CS_final.pdf","access_level":"open_access","relation":"main_file","checksum":"9b9b24351514948d27cec659e632e2cd","creator":"cschwayer","file_size":19226428,"file_id":"7195","content_type":"application/pdf"}]},{"status":"public","day":"16","date_created":"2019-12-17T13:03:41Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"volume":1,"ec_funded":1,"oa_version":"Published Version","doi":"10.1103/physrevresearch.1.033177","publication":"Physical Review Research","issue":"3","oa":1,"date_updated":"2024-02-28T13:11:40Z","article_number":"033177","month":"12","intvolume":"         1","date_published":"2019-12-16T00:00:00Z","year":"2019","external_id":{"arxiv":["1908.02483"]},"quality_controlled":"1","_id":"7190","type":"journal_article","file_date_updated":"2020-07-14T12:47:52Z","arxiv":1,"abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"citation":{"apa":"Huber, D., Hammer, H.-W., &#38; Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">https://doi.org/10.1103/physrevresearch.1.033177</a>","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” <i>Physical Review Research</i>, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">10.1103/physrevresearch.1.033177</a>.","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” <i>Physical Review Research</i>, vol. 1, no. 3. American Physical Society, 2019.","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. <i>Physical Review Research</i>. 2019;1(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">10.1103/physrevresearch.1.033177</a>","chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” <i>Physical Review Research</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevresearch.1.033177\">https://doi.org/10.1103/physrevresearch.1.033177</a>."},"publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"file":[{"file_id":"7193","content_type":"application/pdf","creator":"dernst","file_size":1370022,"access_level":"open_access","relation":"main_file","checksum":"382eb67e62a77052a23887332d363f96","file_name":"2019_PhysRevResearch_Huber.pdf","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-18T07:13:14Z"}],"author":[{"full_name":"Huber, D.","first_name":"D.","last_name":"Huber"},{"first_name":"H.-W.","last_name":"Hammer","full_name":"Hammer, H.-W."},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem"}],"title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"article_processing_charge":"No"},{"title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","author":[{"full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R"},{"first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"first_name":"Daniel J. G.","last_name":"Pearce","full_name":"Pearce, Daniel J. G."},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B"},{"full_name":"Brugués, Jan","last_name":"Brugués","first_name":"Jan"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2019_NatureComm_Caldas.pdf","date_created":"2019-12-23T07:34:56Z","date_updated":"2020-07-14T12:47:53Z","file_id":"7208","content_type":"application/pdf","file_size":8488733,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"a1b44b427ba341383197790d0e8789fa"}],"publisher":"Springer Nature","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"},{"_id":"BjHo"}],"article_processing_charge":"No","quality_controlled":"1","_id":"7197","scopus_import":"1","abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:53Z","type":"journal_article","citation":{"mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>, vol. 10, 5744, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>.","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., &#38; Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>.","ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>","ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744."},"publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","project":[{"name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"oa":1,"date_updated":"2023-09-07T13:18:51Z","article_number":"5744","date_published":"2019-12-17T00:00:00Z","intvolume":"        10","month":"12","year":"2019","external_id":{"isi":["000503009300001"]},"day":"17","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-12-20T12:22:57Z","ddc":["570"],"volume":10,"oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8358"}]},"publication":"Nature Communications","doi":"10.1038/s41467-019-13702-4"},{"year":"2019","external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"page":"1203-1225","date_updated":"2023-10-17T08:53:45Z","issue":"3","oa":1,"intvolume":"        55","month":"09","date_published":"2019-09-25T00:00:00Z","isi":1,"oa_version":"Preprint","ec_funded":1,"doi":"10.1214/18-AIHP916","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","date_created":"2018-12-11T11:44:29Z","status":"public","day":"25","volume":55,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"title":"Limit law of a second class particle in TASEP with non-random initial condition","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ferrari, Patrick","first_name":"Patrick","last_name":"Ferrari"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter"}],"publisher":"Institute of Mathematical Statistics","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"},{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"}],"publication_status":"published","_id":"72","quality_controlled":"1","publication_identifier":{"issn":["0246-0203"]},"citation":{"chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AIHP916\">https://doi.org/10.1214/18-AIHP916</a>.","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2019;55(3):1203-1225. doi:<a href=\"https://doi.org/10.1214/18-AIHP916\">10.1214/18-AIHP916</a>","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:<a href=\"https://doi.org/10.1214/18-AIHP916\">10.1214/18-AIHP916</a>.","apa":"Ferrari, P., Ghosal, P., &#38; Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AIHP916\">https://doi.org/10.1214/18-AIHP916</a>"},"type":"journal_article","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ&lt;λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t."}]},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","orcid":"0000-0002-7969-2729","last_name":"Brighi","full_name":"Brighi, Pietro"},{"last_name":"Grilli","first_name":"Marco","full_name":"Grilli, Marco"},{"last_name":"Leridon","first_name":"Brigitte","full_name":"Leridon, Brigitte"},{"first_name":"Sergio","last_name":"Caprara","full_name":"Caprara, Sergio"}],"title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","publisher":"American Physical Society","publication_status":"published","quality_controlled":"1","_id":"7200","scopus_import":"1","abstract":[{"lang":"eng","text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario)."}],"arxiv":1,"type":"journal_article","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"citation":{"apa":"Brighi, P., Grilli, M., Leridon, B., &#38; Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">https://doi.org/10.1103/PhysRevB.100.174518</a>","mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” <i>Physical Review B</i>, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">10.1103/PhysRevB.100.174518</a>.","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. <i>Physical Review B</i>. 2019;100(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">10.1103/PhysRevB.100.174518</a>","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518.","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” <i>Physical Review B</i>, vol. 100, no. 17. American Physical Society, 2019.","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevB.100.174518\">https://doi.org/10.1103/PhysRevB.100.174518</a>."},"year":"2019","external_id":{"arxiv":["1907.13579"],"isi":["000498845700006"]},"oa":1,"issue":"17","date_updated":"2024-02-28T13:14:08Z","article_number":"174518","date_published":"2019-11-25T00:00:00Z","intvolume":"       100","month":"11","oa_version":"Preprint","isi":1,"publication":"Physical Review B","doi":"10.1103/PhysRevB.100.174518","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.13579"}],"status":"public","day":"25","date_created":"2019-12-22T23:00:41Z","volume":100},{"external_id":{"arxiv":["1802.08021"],"isi":["000545976800011"]},"conference":{"location":"Denver, CO, Unites States","start_date":"2019-11-17","end_date":"2019-11-19","name":"SC: Conference for High Performance Computing, Networking, Storage and Analysis"},"year":"2019","date_published":"2019-11-17T00:00:00Z","month":"11","article_number":"a11","date_updated":"2023-09-06T14:37:55Z","oa":1,"publication":"International Conference for High Performance Computing, Networking, Storage and Analysis, SC","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.08021"}],"doi":"10.1145/3295500.3356222","oa_version":"Preprint","ec_funded":1,"isi":1,"date_created":"2019-12-22T23:00:42Z","status":"public","day":"17","article_processing_charge":"No","department":[{"_id":"DaAl"}],"language":[{"iso":"eng"}],"publisher":"ACM","title":"SparCML: High-performance sparse communication for machine learning","author":[{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"},{"last_name":"Ashkboos","id":"0D0A9058-257B-11EA-A937-9341C3D8BC8A","first_name":"Saleh","full_name":"Ashkboos, Saleh"},{"last_name":"Aghagolzadeh","first_name":"Mehdi","full_name":"Aghagolzadeh, Mehdi"},{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","citation":{"ama":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance sparse communication for machine learning. In: <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3295500.3356222\">10.1145/3295500.3356222</a>","ista":"Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML: High-performance sparse communication for machine learning. International Conference for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference for High Performance Computing, Networking, Storage and Analysis, a11.","short":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:, International Conference for High Performance Computing, Networking, Storage and Analysis, SC, ACM, 2019.","ieee":"C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler, “SparCML: High-performance sparse communication for machine learning,” in <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>, Denver, CO, Unites States, 2019.","chicago":"Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh, and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine Learning.” In <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3295500.3356222\">https://doi.org/10.1145/3295500.3356222</a>.","apa":"Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., &#38; Hoefler, T. (2019). SparCML: High-performance sparse communication for machine learning. In <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>. Denver, CO, Unites States: ACM. <a href=\"https://doi.org/10.1145/3295500.3356222\">https://doi.org/10.1145/3295500.3356222</a>","mla":"Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for Machine Learning.” <i>International Conference for High Performance Computing, Networking, Storage and Analysis, SC</i>, a11, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3295500.3356222\">10.1145/3295500.3356222</a>."},"publication_identifier":{"eissn":["21674337"],"isbn":["9781450362290"],"issn":["21674329"]},"arxiv":1,"abstract":[{"lang":"eng","text":"Applying machine learning techniques to the quickly growing data in science and industry requires highly-scalable algorithms. Large datasets are most commonly processed \"data parallel\" distributed across many nodes. Each node's contribution to the overall gradient is summed using a global allreduce. This allreduce is the single communication and thus scalability bottleneck for most machine learning workloads. We observe that frequently, many gradient values are (close to) zero, leading to sparse of sparsifyable communications. To exploit this insight, we analyze, design, and implement a set of communication-efficient protocols for sparse input data, in conjunction with efficient machine learning algorithms which can leverage these primitives. Our communication protocols generalize standard collective operations, by allowing processes to contribute arbitrary sparse input data vectors. Our generic communication library, SparCML1, extends MPI to support additional features, such as non-blocking (asynchronous) operations and low-precision data representations. As such, SparCML and its techniques will form the basis of future highly-scalable machine learning frameworks."}],"scopus_import":"1","type":"conference","_id":"7201","quality_controlled":"1"},{"article_number":"e51381","intvolume":"         8","month":"11","date_published":"2019-11-18T00:00:00Z","oa":1,"date_updated":"2023-09-06T14:38:39Z","external_id":{"pmid":["31736464"],"isi":["000508156800001"]},"year":"2019","pmid":1,"volume":8,"status":"public","day":"18","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-12-22T23:00:42Z","doi":"10.7554/eLife.51381","publication":"eLife","isi":1,"oa_version":"Published Version","ec_funded":1,"publisher":"eLife Sciences Publications","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:47:53Z","date_created":"2020-02-18T15:19:26Z","file_name":"2019_eLife_Llorca.pdf","relation":"main_file","checksum":"b460ecc33e1a68265e7adea775021f3a","access_level":"open_access","content_type":"application/pdf","file_id":"7503","file_size":2960543,"creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture","author":[{"last_name":"Llorca","first_name":"Alfredo","full_name":"Llorca, Alfredo"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"full_name":"Beattie, Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"full_name":"Wong, Fong Kuan","first_name":"Fong Kuan","last_name":"Wong"},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"full_name":"Serafeimidou-Pouliou, Eleni","first_name":"Eleni","last_name":"Serafeimidou-Pouliou"},{"full_name":"Fernández-Otero, Marian","first_name":"Marian","last_name":"Fernández-Otero"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen"},{"full_name":"Arnold, Sebastian J.","first_name":"Sebastian J.","last_name":"Arnold"},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"last_name":"Maravall","first_name":"Miguel","full_name":"Maravall, Miguel"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"department":[{"_id":"SiHi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:47:53Z","scopus_import":"1","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have investigated the neuronal output of individual progenitor cells in the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. Our experimental results indicate that progenitor cells generate pyramidal cell lineages with a wide range of sizes and laminar configurations. Mathematical modelling indicates that these outcomes are compatible with a stochastic model of cortical neurogenesis in which progenitor cells undergo a series of probabilistic decisions that lead to the specification of very heterogeneous progenies. Our findings support a mechanism for cortical neurogenesis whose flexibility would make it capable to generate the diverse cytoarchitectures that characterize distinct neocortical areas."}],"publication_identifier":{"eissn":["2050084X"]},"citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.51381\">https://doi.org/10.7554/eLife.51381</a>.","ieee":"A. Llorca <i>et al.</i>, “A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. eLife. 8, e51381.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, ELife 8 (2019).","ama":"Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.51381\">10.7554/eLife.51381</a>","mla":"Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.” <i>ELife</i>, vol. 8, e51381, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.51381\">10.7554/eLife.51381</a>.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou, E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly of neocortical cytoarchitecture. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51381\">https://doi.org/10.7554/eLife.51381</a>"},"quality_controlled":"1","_id":"7202","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"FWF","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}]},{"publication":"Communications Biology","doi":"10.1038/s42003-019-0373-y","oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"record":[{"id":"7196","relation":"part_of_dissertation","status":"public"}]},"volume":2,"pmid":1,"day":"23","status":"public","date_created":"2019-12-23T13:36:50Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"external_id":{"pmid":["31044163"],"isi":["000465425700006"]},"year":"2019","article_number":"138","date_published":"2019-04-23T00:00:00Z","month":"04","intvolume":"         2","oa":1,"date_updated":"2023-09-07T13:19:22Z","publication_status":"published","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization."}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:47:53Z","citation":{"short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019).","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2, 138.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure determines the tradeoff between fixation probability and fixation time,” <i>Communications Biology</i>, vol. 2. Springer Nature, 2019.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. <i>Communications Biology</i>. 2019;2. doi:<a href=\"https://doi.org/10.1038/s42003-019-0373-y\">10.1038/s42003-019-0373-y</a>","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” <i>Communications Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42003-019-0373-y\">https://doi.org/10.1038/s42003-019-0373-y</a>.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., &#38; Nowak, M. A. (2019). Population structure determines the tradeoff between fixation probability and fixation time. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-019-0373-y\">https://doi.org/10.1038/s42003-019-0373-y</a>","mla":"Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” <i>Communications Biology</i>, vol. 2, 138, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s42003-019-0373-y\">10.1038/s42003-019-0373-y</a>."},"publication_identifier":{"issn":["2399-3642"]},"quality_controlled":"1","_id":"7210","department":[{"_id":"KrCh"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","title":"Population structure determines the tradeoff between fixation probability and fixation time","author":[{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2019_CommBio_Tkadlec.pdf","date_updated":"2020-07-14T12:47:53Z","date_created":"2019-12-23T13:39:30Z","file_id":"7211","content_type":"application/pdf","creator":"dernst","file_size":1670274,"relation":"main_file","checksum":"d1a69bfe73767e4246f0a38e4e1554dd","access_level":"open_access"}]},{"article_processing_charge":"No","department":[{"_id":"DaAl"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"BMC","title":"Recovering rearranged cancer chromosomes from karyotype graphs","author":[{"last_name":"Aganezov","first_name":"Sergey","full_name":"Aganezov, Sergey"},{"full_name":"Zban, Ilya","first_name":"Ilya","last_name":"Zban"},{"full_name":"Aksenov, Vitalii","first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","last_name":"Aksenov"},{"full_name":"Alexeev, Nikita","last_name":"Alexeev","first_name":"Nikita"},{"first_name":"Michael C.","last_name":"Schatz","full_name":"Schatz, Michael C."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-02T16:10:58Z","file_name":"2019_BMCBioinfo_Aganezov.pdf","relation":"main_file","checksum":"7a30357efdcf8f66587ed495c0927724","access_level":"open_access","creator":"dernst","file_size":1917374,"file_id":"7221","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["14712105"]},"citation":{"chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” <i>BMC Bioinformatics</i>. BMC, 2019. <a href=\"https://doi.org/10.1186/s12859-019-3208-4\">https://doi.org/10.1186/s12859-019-3208-4</a>.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” <i>BMC Bioinformatics</i>, vol. 20. BMC, 2019.","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. <i>BMC Bioinformatics</i>. 2019;20. doi:<a href=\"https://doi.org/10.1186/s12859-019-3208-4\">10.1186/s12859-019-3208-4</a>","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” <i>BMC Bioinformatics</i>, vol. 20, 641, BMC, 2019, doi:<a href=\"https://doi.org/10.1186/s12859-019-3208-4\">10.1186/s12859-019-3208-4</a>.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., &#38; Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. <i>BMC Bioinformatics</i>. BMC. <a href=\"https://doi.org/10.1186/s12859-019-3208-4\">https://doi.org/10.1186/s12859-019-3208-4</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer."}],"type":"journal_article","file_date_updated":"2020-07-14T12:47:54Z","_id":"7214","quality_controlled":"1","external_id":{"isi":["000511618800007"]},"year":"2019","date_published":"2019-12-17T00:00:00Z","month":"12","intvolume":"        20","article_number":"641","date_updated":"2023-09-06T14:51:06Z","oa":1,"publication":"BMC Bioinformatics","doi":"10.1186/s12859-019-3208-4","oa_version":"Published Version","isi":1,"volume":20,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-12-29T23:00:46Z","ddc":["570"],"status":"public","day":"17"},{"language":[{"iso":"eng"}],"article_type":"review","article_processing_charge":"Yes","department":[{"_id":"NanoFab"}],"file":[{"relation":"main_file","access_level":"open_access","checksum":"80f1499e2a4caccdf3aa54b137fd99a0","file_size":2660780,"creator":"dernst","file_id":"7243","content_type":"application/pdf","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:49:59Z","file_name":"2019_Bioengineering_Merrin.pdf"}],"author":[{"full_name":"Merrin, Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"}],"title":"Frontiers in microfluidics, a teaching resource review","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","publisher":"MDPI","publication_status":"published","_id":"7225","quality_controlled":"1","publication_identifier":{"eissn":["23065354"]},"citation":{"short":"J. Merrin, Bioengineering 6 (2019).","ista":"Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering. 6(4), 109.","ieee":"J. Merrin, “Frontiers in microfluidics, a teaching resource review,” <i>Bioengineering</i>, vol. 6, no. 4. MDPI, 2019.","ama":"Merrin J. Frontiers in microfluidics, a teaching resource review. <i>Bioengineering</i>. 2019;6(4). doi:<a href=\"https://doi.org/10.3390/bioengineering6040109\">10.3390/bioengineering6040109</a>","chicago":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” <i>Bioengineering</i>. MDPI, 2019. <a href=\"https://doi.org/10.3390/bioengineering6040109\">https://doi.org/10.3390/bioengineering6040109</a>.","apa":"Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review. <i>Bioengineering</i>. MDPI. <a href=\"https://doi.org/10.3390/bioengineering6040109\">https://doi.org/10.3390/bioengineering6040109</a>","mla":"Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” <i>Bioengineering</i>, vol. 6, no. 4, 109, MDPI, 2019, doi:<a href=\"https://doi.org/10.3390/bioengineering6040109\">10.3390/bioengineering6040109</a>."},"type":"journal_article","file_date_updated":"2020-07-14T12:47:54Z","abstract":[{"lang":"eng","text":"This is a literature teaching resource review for biologically inspired microfluidics courses\r\nor exploring the diverse applications of microfluidics. The structure is around key papers and model\r\norganisms. While courses gradually change over time, a focus remains on understanding how\r\nmicrofluidics has developed as well as what it can and cannot do for researchers. As a primary\r\nstarting point, we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof applications are discussed using model prokaryotic and eukaryotic organisms from the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei), yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms (Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics can still be used effectively for specific applications."}],"scopus_import":"1","year":"2019","external_id":{"pmid":["31816954"],"isi":["000505590000024"]},"date_updated":"2023-09-06T14:52:49Z","issue":"4","oa":1,"month":"12","intvolume":"         6","date_published":"2019-12-03T00:00:00Z","article_number":"109","isi":1,"oa_version":"Published Version","doi":"10.3390/bioengineering6040109","publication":"Bioengineering","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-01-05T23:00:45Z","ddc":["620"],"status":"public","day":"03","pmid":1,"volume":6},{"volume":60,"day":"01","status":"public","ddc":["500"],"date_created":"2020-01-05T23:00:46Z","doi":"10.1063/1.5138135","publication":"Journal of Mathematical Physics","isi":1,"oa_version":"Published Version","article_number":"123504","month":"12","intvolume":"        60","date_published":"2019-12-01T00:00:00Z","issue":"12","oa":1,"date_updated":"2024-02-28T13:01:45Z","external_id":{"isi":["000505529800002"]},"year":"2019","type":"journal_article","file_date_updated":"2020-07-14T12:47:54Z","scopus_import":"1","publication_identifier":{"issn":["00222488"]},"citation":{"ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. <i>Journal of Mathematical Physics</i>. 2019;60(12). doi:<a href=\"https://doi.org/10.1063/1.5138135\">10.1063/1.5138135</a>","ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” <i>Journal of Mathematical Physics</i>, vol. 60, no. 12. AIP Publishing, 2019.","chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5138135\">https://doi.org/10.1063/1.5138135</a>.","apa":"Jaksic, V., &#38; Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5138135\">https://doi.org/10.1063/1.5138135</a>","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” <i>Journal of Mathematical Physics</i>, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5138135\">10.1063/1.5138135</a>."},"quality_controlled":"1","_id":"7226","publication_status":"published","publisher":"AIP Publishing","has_accepted_license":"1","file":[{"access_level":"open_access","relation":"main_file","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","file_id":"7244","content_type":"application/pdf","creator":"dernst","file_size":1025015,"date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:59:13Z","file_name":"2019_JournalMathPhysics_Jaksic.pdf"}],"title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","author":[{"last_name":"Jaksic","first_name":"Vojkan","full_name":"Jaksic, Vojkan"},{"full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"article_processing_charge":"No","article_type":"letter_note","language":[{"iso":"eng"}]},{"oa_version":"Preprint","ec_funded":1,"isi":1,"publication":"27th International Symposium on Graph Drawing and Network Visualization","main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"doi":"10.1007/978-3-030-35802-0_18","day":"28","status":"public","date_created":"2020-01-05T23:00:47Z","volume":11904,"year":"2019","conference":{"name":"GD: Graph Drawing and Network Visualization","start_date":"2019-09-17","end_date":"2019-09-20","location":"Prague, Czech Republic"},"external_id":{"arxiv":["1908.08129"],"isi":["000612918800018"]},"page":"230-243","oa":1,"date_updated":"2023-09-06T14:56:00Z","alternative_title":["LNCS"],"date_published":"2019-11-28T00:00:00Z","intvolume":"     11904","month":"11","publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"quality_controlled":"1","_id":"7230","arxiv":1,"scopus_import":"1","abstract":[{"text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G.","lang":"eng"}],"type":"conference","citation":{"mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” <i>27th International Symposium on Graph Drawing and Network Visualization</i>, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">10.1007/978-3-030-35802-0_18</a>.","apa":"Arroyo Guevara, A. M., Derka, M., &#38; Parada, I. (2019). Extending simple drawings. In <i>27th International Symposium on Graph Drawing and Network Visualization</i> (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">https://doi.org/10.1007/978-3-030-35802-0_18</a>","chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In <i>27th International Symposium on Graph Drawing and Network Visualization</i>, 11904:230–43. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">https://doi.org/10.1007/978-3-030-35802-0_18</a>.","ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: <i>27th International Symposium on Graph Drawing and Network Visualization</i>. Vol 11904. Springer Nature; 2019:230-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-35802-0_18\">10.1007/978-3-030-35802-0_18</a>","ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in <i>27th International Symposium on Graph Drawing and Network Visualization</i>, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243."},"publication_identifier":{"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"article_processing_charge":"No","author":[{"id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","orcid":"0000-0003-2401-8670","last_name":"Arroyo Guevara","full_name":"Arroyo Guevara, Alan M"},{"full_name":"Derka, Martin","last_name":"Derka","first_name":"Martin"},{"full_name":"Parada, Irene","first_name":"Irene","last_name":"Parada"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Extending simple drawings","publisher":"Springer Nature"},{"article_processing_charge":"No","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publisher":"Springer Nature","author":[{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","orcid":"0000-0002-3066-6941","last_name":"Kong"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"],"issn":["0302-9743"]},"citation":{"apa":"Kong, H., Bartocci, E., Jiang, Y., &#38; Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i> (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">https://doi.org/10.1007/978-3-030-29662-9_8</a>","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:<a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">10.1007/978-3-030-29662-9_8</a>.","ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>. Vol 11750. Springer Nature; 2019:123-141. doi:<a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">10.1007/978-3-030-29662-9_8</a>","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In <i>17th International Conference on Formal Modeling and Analysis of Timed Systems</i>, 11750:123–41. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-29662-9_8\">https://doi.org/10.1007/978-3-030-29662-9_8</a>."},"type":"conference","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature."}],"_id":"7231","quality_controlled":"1","page":"123-141","external_id":{"isi":["000611677700008"],"arxiv":["1907.11514"]},"conference":{"location":"Amsterdam, The Netherlands","start_date":"2019-08-27","end_date":"2019-08-29","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"year":"2019","intvolume":"     11750","month":"08","alternative_title":["LNCS"],"date_published":"2019-08-13T00:00:00Z","date_updated":"2023-09-06T14:55:15Z","oa":1,"doi":"10.1007/978-3-030-29662-9_8","main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","isi":1,"oa_version":"Preprint","volume":11750,"date_created":"2020-01-05T23:00:47Z","day":"13","status":"public"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","page":"2559-2568","year":"2019","date_published":"2019-08-01T00:00:00Z","intvolume":"        12","month":"08","oa":1,"issue":"8","date_updated":"2021-01-12T08:12:41Z","publication":"Energy & Environmental Science","doi":"10.1039/c9ee01453e","oa_version":"Published Version","volume":12,"day":"01","status":"public","ddc":["530","541","540"],"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"date_created":"2020-01-15T07:18:04Z","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"RSC","has_accepted_license":"1","author":[{"last_name":"Mourad","first_name":"Eléonore","full_name":"Mourad, Eléonore"},{"full_name":"Petit, Yann K.","last_name":"Petit","first_name":"Yann K."},{"first_name":"Riccardo","last_name":"Spezia","full_name":"Spezia, Riccardo"},{"full_name":"Samojlov, Aleksej","first_name":"Aleksej","last_name":"Samojlov"},{"last_name":"Summa","first_name":"Francesco F.","full_name":"Summa, Francesco F."},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"last_name":"Leypold","first_name":"Christian","full_name":"Leypold, Christian"},{"first_name":"Nika","last_name":"Mahne","full_name":"Mahne, Nika"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"full_name":"Brutti, Sergio","first_name":"Sergio","last_name":"Brutti"},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319"}],"title":"Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2019_EnergyEnvironScienc_Mourad.pdf","date_created":"2020-01-30T16:11:05Z","date_updated":"2020-07-14T12:47:55Z","creator":"dernst","file_size":2888027,"file_id":"7424","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"94d4cfb2ab0b4c90ef76a7f3cc811feb"}],"publication_status":"published","abstract":[{"text":"Aprotic alkali metal–oxygen batteries require reversible formation of metal superoxide or peroxide on cycling. Severe parasitic reactions cause poor rechargeability, efficiency, and cycle life and have been shown to be caused by singlet oxygen (1O2) that forms at all stages of cycling. However, its formation mechanism remains unclear. We show that disproportionation of superoxide, the product or intermediate on discharge and charge, to peroxide and oxygen is responsible for 1O2 formation. While the overall reaction is driven by the stability of peroxide and thus favored by stronger Lewis acidic cations such as Li+, the 1O2 fraction is enhanced by weak Lewis acids such as organic cations. Concurrently, the metal peroxide yield drops with increasing 1O2. The results explain a major parasitic pathway during cell cycling and the growing severity in K–, Na–, and Li–O2 cells based on the growing propensity for disproportionation. High capacities and rates with peroxides are now realized to require solution processes, which form peroxide or release O2via disproportionation. The results therefore establish the central dilemma that disproportionation is required for high capacity but also responsible for irreversible reactions. Highly reversible cell operation requires hence finding reaction routes that avoid disproportionation.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:55Z","type":"journal_article","extern":"1","citation":{"apa":"Mourad, E., Petit, Y. K., Spezia, R., Samojlov, A., Summa, F. F., Prehal, C., … Freunberger, S. A. (2019). Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. <i>Energy &#38; Environmental Science</i>. RSC. <a href=\"https://doi.org/10.1039/c9ee01453e\">https://doi.org/10.1039/c9ee01453e</a>","mla":"Mourad, Eléonore, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.” <i>Energy &#38; Environmental Science</i>, vol. 12, no. 8, RSC, 2019, pp. 2559–68, doi:<a href=\"https://doi.org/10.1039/c9ee01453e\">10.1039/c9ee01453e</a>.","ista":"Mourad E, Petit YK, Spezia R, Samojlov A, Summa FF, Prehal C, Leypold C, Mahne N, Slugovc C, Fontaine O, Brutti S, Freunberger SA. 2019. Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy &#38; Environmental Science. 12(8), 2559–2568.","short":"E. Mourad, Y.K. Petit, R. Spezia, A. Samojlov, F.F. Summa, C. Prehal, C. Leypold, N. Mahne, C. Slugovc, O. Fontaine, S. Brutti, S.A. Freunberger, Energy &#38; Environmental Science 12 (2019) 2559–2568.","ieee":"E. Mourad <i>et al.</i>, “Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries,” <i>Energy &#38; Environmental Science</i>, vol. 12, no. 8. RSC, pp. 2559–2568, 2019.","ama":"Mourad E, Petit YK, Spezia R, et al. Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. <i>Energy &#38; Environmental Science</i>. 2019;12(8):2559-2568. doi:<a href=\"https://doi.org/10.1039/c9ee01453e\">10.1039/c9ee01453e</a>","chicago":"Mourad, Eléonore, Yann K. Petit, Riccardo Spezia, Aleksej Samojlov, Francesco F. Summa, Christian Prehal, Christian Leypold, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.” <i>Energy &#38; Environmental Science</i>. RSC, 2019. <a href=\"https://doi.org/10.1039/c9ee01453e\">https://doi.org/10.1039/c9ee01453e</a>."},"publication_identifier":{"issn":["1754-5692","1754-5706"]},"quality_controlled":"1","_id":"7275"},{"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Wiley","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells","author":[{"first_name":"Yann K.","last_name":"Petit","full_name":"Petit, Yann K."},{"first_name":"Christian","last_name":"Leypold","full_name":"Leypold, Christian"},{"first_name":"Nika","last_name":"Mahne","full_name":"Mahne, Nika"},{"first_name":"Eléonore","last_name":"Mourad","full_name":"Mourad, Eléonore"},{"full_name":"Schafzahl, Lukas","first_name":"Lukas","last_name":"Schafzahl"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"last_name":"Borisov","first_name":"Sergey M.","full_name":"Borisov, Sergey M."},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"file":[{"checksum":"9620b6a511a910d7abe1f26c42dc7f83","relation":"main_file","access_level":"open_access","file_size":952737,"creator":"dernst","file_id":"7356","content_type":"application/pdf","date_updated":"2020-07-14T12:47:55Z","date_created":"2020-01-22T16:16:54Z","file_name":"2019_AngewChemie_Petit.pdf"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Singlet oxygen (1O2) causes a major fraction of the parasitic chemistry during the cycling of non‐aqueous alkali metal‐O2 batteries and also contributes to interfacial reactivity of transition‐metal oxide intercalation compounds. We introduce DABCOnium, the mono alkylated form of 1,4‐diazabicyclo[2.2.2]octane (DABCO), as an efficient 1O2 quencher with an unusually high oxidative stability of ca. 4.2 V vs. Li/Li+. Previous quenchers are strongly Lewis basic amines with too low oxidative stability. DABCOnium is an ionic liquid, non‐volatile, highly soluble in the electrolyte, stable against superoxide and peroxide, and compatible with lithium metal. The electrochemical stability covers the required range for metal–O2 batteries and greatly reduces 1O2 related parasitic chemistry as demonstrated for the Li–O2 cell."}],"file_date_updated":"2020-07-14T12:47:55Z","type":"journal_article","extern":"1","citation":{"mla":"Petit, Yann K., et al. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” <i>Angewandte Chemie International Edition</i>, vol. 58, no. 20, Wiley, 2019, pp. 6535–39, doi:<a href=\"https://doi.org/10.1002/anie.201901869\">10.1002/anie.201901869</a>.","apa":"Petit, Y. K., Leypold, C., Mahne, N., Mourad, E., Schafzahl, L., Slugovc, C., … Freunberger, S. A. (2019). DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201901869\">https://doi.org/10.1002/anie.201901869</a>","chicago":"Petit, Yann K., Christian Leypold, Nika Mahne, Eléonore Mourad, Lukas Schafzahl, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” <i>Angewandte Chemie International Edition</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/anie.201901869\">https://doi.org/10.1002/anie.201901869</a>.","ama":"Petit YK, Leypold C, Mahne N, et al. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. <i>Angewandte Chemie International Edition</i>. 2019;58(20):6535-6539. doi:<a href=\"https://doi.org/10.1002/anie.201901869\">10.1002/anie.201901869</a>","ieee":"Y. K. Petit <i>et al.</i>, “DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells,” <i>Angewandte Chemie International Edition</i>, vol. 58, no. 20. Wiley, pp. 6535–6539, 2019.","ista":"Petit YK, Leypold C, Mahne N, Mourad E, Schafzahl L, Slugovc C, Borisov SM, Freunberger SA. 2019. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 58(20), 6535–6539.","short":"Y.K. Petit, C. Leypold, N. Mahne, E. Mourad, L. Schafzahl, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie International Edition 58 (2019) 6535–6539."},"publication_identifier":{"issn":["1433-7851"]},"quality_controlled":"1","_id":"7276","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"6535-6539","year":"2019","date_published":"2019-05-13T00:00:00Z","month":"05","intvolume":"        58","oa":1,"issue":"20","date_updated":"2021-01-12T08:12:42Z","publication":"Angewandte Chemie International Edition","doi":"10.1002/anie.201901869","oa_version":"Published Version","volume":58,"status":"public","day":"13","ddc":["540"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2020-01-15T07:19:27Z"},{"oa_version":"Published Version","doi":"10.1038/s41467-019-09399-0","publication":"Nature Communications","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-01-15T12:12:26Z","ddc":["540"],"day":"26","status":"public","volume":10,"year":"2019","date_updated":"2021-01-12T08:12:44Z","oa":1,"month":"03","intvolume":"        10","date_published":"2019-03-26T00:00:00Z","article_number":"1380","publication_status":"published","_id":"7280","quality_controlled":"1","citation":{"chicago":"Kwak, Won-Jin, Hun Kim, Yann K. Petit, Christian Leypold, Trung Thien Nguyen, Nika Mahne, Paul Redfern, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09399-0\">https://doi.org/10.1038/s41467-019-09399-0</a>.","ama":"Kwak W-J, Kim H, Petit YK, et al. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-09399-0\">10.1038/s41467-019-09399-0</a>","short":"W.-J. Kwak, H. Kim, Y.K. Petit, C. Leypold, T.T. Nguyen, N. Mahne, P. Redfern, L.A. Curtiss, H.-G. Jung, S.M. Borisov, S.A. Freunberger, Y.-K. Sun, Nature Communications 10 (2019).","ista":"Kwak W-J, Kim H, Petit YK, Leypold C, Nguyen TT, Mahne N, Redfern P, Curtiss LA, Jung H-G, Borisov SM, Freunberger SA, Sun Y-K. 2019. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 10, 1380.","ieee":"W.-J. Kwak <i>et al.</i>, “Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","mla":"Kwak, Won-Jin, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” <i>Nature Communications</i>, vol. 10, 1380, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09399-0\">10.1038/s41467-019-09399-0</a>.","apa":"Kwak, W.-J., Kim, H., Petit, Y. K., Leypold, C., Nguyen, T. T., Mahne, N., … Sun, Y.-K. (2019). Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09399-0\">https://doi.org/10.1038/s41467-019-09399-0</a>"},"publication_identifier":{"issn":["2041-1723"]},"extern":"1","type":"journal_article","file_date_updated":"2020-07-14T12:47:55Z","abstract":[{"text":"Non-aqueous lithium-oxygen batteries cycle by forming lithium peroxide during discharge and oxidizing it during recharge. The significant problem of oxidizing the solid insulating lithium peroxide can greatly be facilitated by incorporating redox mediators that shuttle electron-holes between the porous substrate and lithium peroxide. Redox mediator stability is thus key for energy efficiency, reversibility, and cycle life. However, the gradual deactivation of redox mediators during repeated cycling has not conclusively been explained. Here, we show that organic redox mediators are predominantly decomposed by singlet oxygen that forms during cycling. Their reaction with superoxide, previously assumed to mainly trigger their degradation, peroxide, and dioxygen, is orders of magnitude slower in comparison. The reduced form of the mediator is markedly more reactive towards singlet oxygen than the oxidized form, from which we derive reaction mechanisms supported by density functional theory calculations. Redox mediators must thus be designed for stability against singlet oxygen.","lang":"eng"}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","file":[{"date_created":"2020-01-22T15:58:54Z","date_updated":"2020-07-14T12:47:55Z","file_name":"2019_NatureComm_Kwak.pdf","relation":"main_file","checksum":"123dd33e7f26761c82c74e10811a1e4d","access_level":"open_access","file_id":"7355","content_type":"application/pdf","creator":"dernst","file_size":1003676}],"author":[{"full_name":"Kwak, Won-Jin","last_name":"Kwak","first_name":"Won-Jin"},{"full_name":"Kim, Hun","last_name":"Kim","first_name":"Hun"},{"first_name":"Yann K.","last_name":"Petit","full_name":"Petit, Yann K."},{"full_name":"Leypold, Christian","last_name":"Leypold","first_name":"Christian"},{"last_name":"Nguyen","first_name":"Trung Thien","full_name":"Nguyen, Trung Thien"},{"full_name":"Mahne, Nika","last_name":"Mahne","first_name":"Nika"},{"full_name":"Redfern, Paul","last_name":"Redfern","first_name":"Paul"},{"full_name":"Curtiss, Larry A.","first_name":"Larry A.","last_name":"Curtiss"},{"last_name":"Jung","first_name":"Hun-Gi","full_name":"Jung, Hun-Gi"},{"first_name":"Sergey M.","last_name":"Borisov","full_name":"Borisov, Sergey M."},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"last_name":"Sun","first_name":"Yang-Kook","full_name":"Sun, Yang-Kook"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen","has_accepted_license":"1","publisher":"Springer Nature"},{"year":"2019","page":"9914-9922","issue":"11","oa":1,"date_updated":"2021-01-12T08:12:44Z","intvolume":"         9","month":"11","date_published":"2019-11-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1021/acscatal.9b01337","publication":"ACS Catalysis","status":"public","day":"01","date_created":"2020-01-15T12:12:40Z","ddc":["540"],"volume":9,"article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","file":[{"relation":"main_file","checksum":"bbaebfe5ff0bcab6235821ba3460b7de","access_level":"open_access","file_size":1199086,"creator":"sfreunbe","file_id":"8053","content_type":"application/pdf","date_created":"2020-06-29T15:19:30Z","date_updated":"2020-07-14T12:47:55Z","file_name":"Revised Manuscript.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kwak, Won-Jin","first_name":"Won-Jin","last_name":"Kwak"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"full_name":"Kim, Hun","first_name":"Hun","last_name":"Kim"},{"first_name":"Jiwon","last_name":"Park","full_name":"Park, Jiwon"},{"full_name":"Nguyen, Trung Thien","first_name":"Trung Thien","last_name":"Nguyen"},{"full_name":"Jung, Hun-Gi","last_name":"Jung","first_name":"Hun-Gi"},{"first_name":"Hye Ryung","last_name":"Byon","full_name":"Byon, Hye Ryung"},{"last_name":"Sun","first_name":"Yang-Kook","full_name":"Sun, Yang-Kook"}],"title":"Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries","publisher":"ACS","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","_id":"7281","file_date_updated":"2020-07-14T12:47:55Z","type":"journal_article","abstract":[{"lang":"eng","text":"Li–O2 batteries are plagued by side reactions that cause poor rechargeability and efficiency. These reactions were recently revealed to be predominantly caused by singlet oxygen, which can be neutralized by chemical traps or physical quenchers. However, traps are irreversibly consumed and thus only active for a limited time, and so far identified quenchers lack oxidative stability to be suitable for typically required recharge potentials. Thus, reducing the charge potential within the stability limit of the quencher and/or finding more stable quenchers is required. Here, we show that dimethylphenazine as a redox mediator decreases the charge potential well within the stability limit of the quencher 1,4-diazabicyclo[2.2.2]octane. The quencher can thus mitigate the parasitic reactions without being oxidatively decomposed. At the same time the quencher protects the redox mediator from singlet oxygen attack. The mutual conservation of the redox mediator and the quencher is rational for stable and effective Li–O2 batteries."}],"publication_identifier":{"issn":["2155-5435"]},"extern":"1","citation":{"short":"W.-J. Kwak, S.A. Freunberger, H. Kim, J. Park, T.T. Nguyen, H.-G. Jung, H.R. Byon, Y.-K. Sun, ACS Catalysis 9 (2019) 9914–9922.","ieee":"W.-J. Kwak <i>et al.</i>, “Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries,” <i>ACS Catalysis</i>, vol. 9, no. 11. ACS, pp. 9914–9922, 2019.","ista":"Kwak W-J, Freunberger SA, Kim H, Park J, Nguyen TT, Jung H-G, Byon HR, Sun Y-K. 2019. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 9(11), 9914–9922.","ama":"Kwak W-J, Freunberger SA, Kim H, et al. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. <i>ACS Catalysis</i>. 2019;9(11):9914-9922. doi:<a href=\"https://doi.org/10.1021/acscatal.9b01337\">10.1021/acscatal.9b01337</a>","chicago":"Kwak, Won-Jin, Stefan Alexander Freunberger, Hun Kim, Jiwon Park, Trung Thien Nguyen, Hun-Gi Jung, Hye Ryung Byon, and Yang-Kook Sun. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” <i>ACS Catalysis</i>. ACS, 2019. <a href=\"https://doi.org/10.1021/acscatal.9b01337\">https://doi.org/10.1021/acscatal.9b01337</a>.","apa":"Kwak, W.-J., Freunberger, S. A., Kim, H., Park, J., Nguyen, T. T., Jung, H.-G., … Sun, Y.-K. (2019). Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. <i>ACS Catalysis</i>. ACS. <a href=\"https://doi.org/10.1021/acscatal.9b01337\">https://doi.org/10.1021/acscatal.9b01337</a>","mla":"Kwak, Won-Jin, et al. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” <i>ACS Catalysis</i>, vol. 9, no. 11, ACS, 2019, pp. 9914–22, doi:<a href=\"https://doi.org/10.1021/acscatal.9b01337\">10.1021/acscatal.9b01337</a>."}},{"file":[{"file_id":"8054","content_type":"application/pdf","creator":"sfreunbe","file_size":286805,"relation":"main_file","checksum":"76806cff3d5b62f846499a8617cee7ef","access_level":"open_access","file_name":"Freunberger on Eichhorn.pdf","date_created":"2020-06-29T15:38:21Z","date_updated":"2020-07-14T12:47:55Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interphase identity crisis","author":[{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"}],"publisher":"Springer Nature","has_accepted_license":"1","article_type":"letter_note","language":[{"iso":"eng"}],"article_processing_charge":"No","quality_controlled":"1","_id":"7282","type":"journal_article","file_date_updated":"2020-07-14T12:47:55Z","abstract":[{"text":"Interphases that form on the anode surface of lithium-ion batteries are critical for performance and lifetime, but are poorly understood. Now, a decade-old misconception regarding a main component of the interphase has been revealed, which could potentially lead to improved devices.","lang":"eng"}],"publication_identifier":{"issn":["1755-4330","1755-4349"]},"extern":"1","citation":{"ista":"Freunberger SA. 2019. Interphase identity crisis. Nature Chemistry. 11(9), 761–763.","short":"S.A. Freunberger, Nature Chemistry 11 (2019) 761–763.","ieee":"S. A. Freunberger, “Interphase identity crisis,” <i>Nature Chemistry</i>, vol. 11, no. 9. Springer Nature, pp. 761–763, 2019.","ama":"Freunberger SA. Interphase identity crisis. <i>Nature Chemistry</i>. 2019;11(9):761-763. doi:<a href=\"https://doi.org/10.1038/s41557-019-0311-0\">10.1038/s41557-019-0311-0</a>","chicago":"Freunberger, Stefan Alexander. “Interphase Identity Crisis.” <i>Nature Chemistry</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41557-019-0311-0\">https://doi.org/10.1038/s41557-019-0311-0</a>.","apa":"Freunberger, S. A. (2019). Interphase identity crisis. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-019-0311-0\">https://doi.org/10.1038/s41557-019-0311-0</a>","mla":"Freunberger, Stefan Alexander. “Interphase Identity Crisis.” <i>Nature Chemistry</i>, vol. 11, no. 9, Springer Nature, 2019, pp. 761–63, doi:<a href=\"https://doi.org/10.1038/s41557-019-0311-0\">10.1038/s41557-019-0311-0</a>."},"publication_status":"published","issue":"9","oa":1,"date_updated":"2021-01-12T08:12:44Z","month":"08","intvolume":"        11","date_published":"2019-08-19T00:00:00Z","year":"2019","page":"761-763","day":"19","status":"public","ddc":["540","547"],"date_created":"2020-01-15T12:12:53Z","volume":11,"oa_version":"Submitted Version","doi":"10.1038/s41557-019-0311-0","publication":"Nature Chemistry"}]