[{"quality_controlled":"1","citation":{"apa":"Salzer, E., Çaǧdaş, D., Hons, M., Mace, E., Garncarz, W., Petronczki, O., … Boztug, K. (2016). RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>","ista":"Salzer E, Çaǧdaş D, Hons M, Mace E, Garncarz W, Petronczki O, Platzer R, Pfajfer L, Bilic I, Ban S, Willmann K, Mukherjee M, Supper V, Hsu H, Banerjee P, Sinha P, Mcclanahan F, Zlabinger G, Pickl W, Gribben J, Stockinger H, Bennett K, Huppa J, Dupré L, Sanal Ö, Jäger U, Sixt MK, Tezcan I, Orange J, Boztug K. 2016. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nature Immunology. 17(12), 1352–1360.","short":"E. Salzer, D. Çaǧdaş, M. Hons, E. Mace, W. Garncarz, O. Petronczki, R. Platzer, L. Pfajfer, I. Bilic, S. Ban, K. Willmann, M. Mukherjee, V. Supper, H. Hsu, P. Banerjee, P. Sinha, F. Mcclanahan, G. Zlabinger, W. Pickl, J. Gribben, H. Stockinger, K. Bennett, J. Huppa, L. Dupré, Ö. Sanal, U. Jäger, M.K. Sixt, I. Tezcan, J. Orange, K. Boztug, Nature Immunology 17 (2016) 1352–1360.","ieee":"E. Salzer <i>et al.</i>, “RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1352–1360, 2016.","ama":"Salzer E, Çaǧdaş D, Hons M, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. <i>Nature Immunology</i>. 2016;17(12):1352-1360. doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>","chicago":"Salzer, Elisabeth, Deniz Çaǧdaş, Miroslav Hons, Emily Mace, Wojciech Garncarz, Oezlem Petronczki, René Platzer, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3575\">https://doi.org/10.1038/ni.3575</a>.","mla":"Salzer, Elisabeth, et al. “RASGRP1 Deficiency Causes Immunodeficiency with Impaired Cytoskeletal Dynamics.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1352–60, doi:<a href=\"https://doi.org/10.1038/ni.3575\">10.1038/ni.3575</a>."},"issue":"12","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263"}],"doi":"10.1038/ni.3575","pmid":1,"page":"1352 - 1360","external_id":{"isi":["000388056400005"],"pmid":["27776107"]},"abstract":[{"lang":"eng","text":"RASGRP1 is an important guanine nucleotide exchange factor and activator of the RAS-MAPK pathway following T cell antigen receptor (TCR) signaling. The consequences of RASGRP1 mutations in humans are unknown. In a patient with recurrent bacterial and viral infections, born to healthy consanguineous parents, we used homozygosity mapping and exome sequencing to identify a biallelic stop-gain variant in RASGRP1. This variant segregated perfectly with the disease and has not been reported in genetic databases. RASGRP1 deficiency was associated in T cells and B cells with decreased phosphorylation of the extracellular-signal-regulated serine kinase ERK, which was restored following expression of wild-type RASGRP1. RASGRP1 deficiency also resulted in defective proliferation, activation and motility of T cells and B cells. RASGRP1-deficient natural killer (NK) cells exhibited impaired cytotoxicity with defective granule convergence and actin accumulation. Interaction proteomics identified the dynein light chain DYNLL1 as interacting with RASGRP1, which links RASGRP1 to cytoskeletal dynamics. RASGRP1-deficient cells showed decreased activation of the GTPase RhoA. Treatment with lenalidomide increased RhoA activity and reversed the migration and activation defects of RASGRP1-deficient lymphocytes."}],"publisher":"Nature Publishing Group","scopus_import":"1","_id":"1137","oa_version":"Submitted Version","date_updated":"2025-09-22T14:13:22Z","oa":1,"intvolume":"        17","department":[{"_id":"MiSi"}],"author":[{"last_name":"Salzer","first_name":"Elisabeth","full_name":"Salzer, Elisabeth"},{"full_name":"Çaǧdaş, Deniz","first_name":"Deniz","last_name":"Çaǧdaş"},{"last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348"},{"full_name":"Mace, Emily","last_name":"Mace","first_name":"Emily"},{"first_name":"Wojciech","last_name":"Garncarz","full_name":"Garncarz, Wojciech"},{"full_name":"Petronczki, Oezlem","first_name":"Oezlem","last_name":"Petronczki"},{"first_name":"René","last_name":"Platzer","full_name":"Platzer, René"},{"full_name":"Pfajfer, Laurène","last_name":"Pfajfer","first_name":"Laurène"},{"full_name":"Bilic, Ivan","last_name":"Bilic","first_name":"Ivan"},{"last_name":"Ban","first_name":"Sol","full_name":"Ban, Sol"},{"last_name":"Willmann","first_name":"Katharina","full_name":"Willmann, Katharina"},{"last_name":"Mukherjee","first_name":"Malini","full_name":"Mukherjee, Malini"},{"full_name":"Supper, Verena","last_name":"Supper","first_name":"Verena"},{"full_name":"Hsu, Hsiangting","last_name":"Hsu","first_name":"Hsiangting"},{"first_name":"Pinaki","last_name":"Banerjee","full_name":"Banerjee, Pinaki"},{"last_name":"Sinha","first_name":"Papiya","full_name":"Sinha, Papiya"},{"first_name":"Fabienne","last_name":"Mcclanahan","full_name":"Mcclanahan, Fabienne"},{"first_name":"Gerhard","last_name":"Zlabinger","full_name":"Zlabinger, Gerhard"},{"full_name":"Pickl, Winfried","last_name":"Pickl","first_name":"Winfried"},{"first_name":"John","last_name":"Gribben","full_name":"Gribben, John"},{"full_name":"Stockinger, Hannes","first_name":"Hannes","last_name":"Stockinger"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"full_name":"Huppa, Johannes","last_name":"Huppa","first_name":"Johannes"},{"full_name":"Dupré, Loï̈C","first_name":"Loï̈C","last_name":"Dupré"},{"last_name":"Sanal","first_name":"Özden","full_name":"Sanal, Özden"},{"first_name":"Ulrich","last_name":"Jäger","full_name":"Jäger, Ulrich"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Tezcan, Ilhan","first_name":"Ilhan","last_name":"Tezcan"},{"full_name":"Orange, Jordan","first_name":"Jordan","last_name":"Orange"},{"first_name":"Kaan","last_name":"Boztug","full_name":"Boztug, Kaan"}],"date_published":"2016-12-01T00:00:00Z","month":"12","article_type":"original","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"6221","type":"journal_article","article_processing_charge":"No","title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","publication":"Nature Immunology","publication_status":"published","isi":1,"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:21Z","volume":17,"day":"01","year":"2016"},{"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:21Z","conference":{"name":"LICS: Logic in Computer Science","location":"New York, NY, USA","end_date":"2016-07-08","start_date":"2016-07-05"},"year":"2016","day":"05","title":"Quantitative automata under probabilistic semantics","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","article_processing_charge":"No","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","publication_status":"published","isi":1,"ec_funded":1,"oa":1,"date_updated":"2025-09-22T14:12:47Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"arxiv":1,"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"date_published":"2016-07-05T00:00:00Z","month":"07","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","publist_id":"6220","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1604.06764","open_access":"1"}],"citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>"},"doi":"10.1145/2933575.2933588","abstract":[{"text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider. © 2016 ACM.","lang":"eng"}],"page":"76 - 85","external_id":{"arxiv":["1604.06764"],"isi":["000387609200008"]},"publisher":"IEEE","scopus_import":"1","oa_version":"Preprint","_id":"1138"},{"day":"05","year":"2016","conference":{"name":"LICS: Logic in Computer Science","location":"New York, NY, USA","end_date":"2016-07-08","start_date":"2016-07-05"},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:22Z","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"isi":1,"article_processing_charge":"No","title":"Model and objective separation with conditional lower bounds: disjunction is harder than conjunction","acknowledgement":"K.  C.,  M.  H.,  and  W.  D.  are  partially  supported  by  the  Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003.\r\nK. C. is partially supported by the Austrian Science Fund (FWF)\r\nNFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant\r\n(279307: Graph Games). For W. D., M. H., and V. L. the research\r\nleading to these results has received funding from the European\r\nResearch Council under the European Union’s Seventh Framework\r\nProgramme (FP/2007-2013) / ERC Grant Agreement no. 340506.","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","publication_status":"published","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Wolfgang","last_name":"Dvoák","full_name":"Dvoák, Wolfgang"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"date_published":"2016-07-05T00:00:00Z","month":"07","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"6219","type":"conference","date_updated":"2025-09-22T14:12:05Z","oa":1,"arxiv":1,"department":[{"_id":"KrCh"}],"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"external_id":{"arxiv":["1602.02670"],"isi":["000387609200020"]},"page":"197 - 206","abstract":[{"text":"Given a model of a system and an objective, the model-checking question asks whether the model satisfies the objective. We study polynomial-time problems in two classical models, graphs and Markov Decision Processes (MDPs), with respect to several fundamental -regular objectives, e.g., Rabin and Streett objectives. For many of these problems the best-known upper bounds are quadratic or cubic, yet no super-linear lower bounds are known. In this work our contributions are two-fold: First, we present several improved algorithms, and second, we present the first conditional super-linear lower bounds based on widely believed assumptions about the complexity of CNF-SAT and combinatorial Boolean matrix multiplication. A separation result for two models with respect to an objective means a conditional lower bound for one model that is strictly higher than the existing upper bound for the other model, and similarly for two objectives with respect to a model. Our results establish the following separation results: (1) A separation of models (graphs and MDPs) for disjunctive queries of reachability and Büchi objectives. (2) Two kinds of separations of objectives, both for graphs and MDPs, namely, (2a) the separation of dual objectives such as Streett/Rabin objectives, and (2b) the separation of conjunction and disjunction of multiple objectives of the same type such as safety, Büchi, and coBüchi. In summary, our results establish the first model and objective separation results for graphs and MDPs for various classical -regular objectives. Quite strikingly, we establish conditional lower bounds for the disjunction of objectives that are strictly higher than the existing upper bounds for the conjunction of the same objectives. © 2016 ACM.","lang":"eng"}],"publisher":"IEEE","scopus_import":"1","_id":"1140","oa_version":"Preprint","quality_controlled":"1","citation":{"short":"K. Chatterjee, W. Dvoák, M. Henzinger, V. Loitzenbauer, in:, Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2016, pp. 197–206.","ista":"Chatterjee K, Dvoák W, Henzinger M, Loitzenbauer V. 2016. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, , 197–206.","apa":"Chatterjee, K., Dvoák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 197–206). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>","mla":"Chatterjee, Krishnendu, et al. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2016, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvoák, Monika Henzinger, and Veronika Loitzenbauer. “Model and Objective Separation with Conditional Lower Bounds: Disjunction Is Harder than Conjunction.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 197–206. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2935304\">https://doi.org/10.1145/2933575.2935304</a>.","ama":"Chatterjee K, Dvoák W, Henzinger M, Loitzenbauer V. Model and objective separation with conditional lower bounds: disjunction is harder than conjunction. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2016:197-206. doi:<a href=\"https://doi.org/10.1145/2933575.2935304\">10.1145/2933575.2935304</a>","ieee":"K. Chatterjee, W. Dvoák, M. Henzinger, and V. Loitzenbauer, “Model and objective separation with conditional lower bounds: disjunction is harder than conjunction,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science</i>, New York, NY, USA, 2016, pp. 197–206."},"main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"doi":"10.1145/2933575.2935304"},{"volume":17,"day":"01","year":"2016","date_created":"2018-12-11T11:50:22Z","language":[{"iso":"eng"}],"isi":1,"publication":"Nature Immunology","article_processing_charge":"No","acknowledgement":"Y. Fukui (Medical Institute of Bioregulation, Kyushu University) and J. Stein (Theodor Kocher Institute, University of Bern) are acknowledged for providing the DOCK8 deficient bone marrow. and H. Häcker (St. Judes Children's Research Hospital) for providing the ERHBD-HoxB8-encoding retroviral construct. pSpCas9(BB)-2a-Puro (PX459) was a gift from F. Zhang (Massachusetts Institute of Technology) (Addgene plasmid # 48139) and pGRG36 was a gift from N. Craig (Johns Hopkins University School of Medicine) (Addgene plasmid # 16666). LifeAct-GFP-encoding retrovirus was kindly provided by A. Leithner (Institute of Science and Technology Austria). pSIM8 and TKC E. coli were gifts from D.L. Court (Center for Cancer Research, National Cancer Institute). We acknowledge M. Gröger and S. Rauscher for excellent technical support (Core imaging facility, Medical University of Vienna). We thank D.P. Barlow and L.R. Cheever for critical reading of the manuscript. This work was supported by the Austrian Academy of Sciences, the Science Fund of the Austrian National Bank (14107) and the Austrian Science Fund FWF (I1620-B22) in the Infect-ERA framework (to S.Knapp).","title":"Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions","publication_status":"published","author":[{"full_name":"Martins, Rui","last_name":"Martins","first_name":"Rui"},{"full_name":"Maier, Julia","first_name":"Julia","last_name":"Maier"},{"full_name":"Gorki, Anna","last_name":"Gorki","first_name":"Anna"},{"full_name":"Huber, Kilian","last_name":"Huber","first_name":"Kilian"},{"last_name":"Sharif","first_name":"Omar","full_name":"Sharif, Omar"},{"full_name":"Starkl, Philipp","last_name":"Starkl","first_name":"Philipp"},{"first_name":"Simona","last_name":"Saluzzo","full_name":"Saluzzo, Simona"},{"full_name":"Quattrone, Federica","first_name":"Federica","last_name":"Quattrone"},{"full_name":"Gawish, Riem","last_name":"Gawish","first_name":"Riem"},{"last_name":"Lakovits","first_name":"Karin","full_name":"Lakovits, Karin"},{"last_name":"Aichinger","first_name":"Michael","full_name":"Aichinger, Michael"},{"full_name":"Radic Sarikas, Branka","first_name":"Branka","last_name":"Radic Sarikas"},{"full_name":"Lardeau, Charles","first_name":"Charles","last_name":"Lardeau"},{"full_name":"Hladik, Anastasiya","last_name":"Hladik","first_name":"Anastasiya"},{"full_name":"Korosec, Ana","first_name":"Ana","last_name":"Korosec"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari"},{"last_name":"Duggan","first_name":"Michelle","full_name":"Duggan, Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"first_name":"Harald","last_name":"Esterbauer","full_name":"Esterbauer, Harald"},{"full_name":"Colinge, Jacques","first_name":"Jacques","last_name":"Colinge"},{"first_name":"Stephanie","last_name":"Eisenbarth","full_name":"Eisenbarth, Stephanie"},{"full_name":"Decker, Thomas","last_name":"Decker","first_name":"Thomas"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"first_name":"Stefan","last_name":"Kubicek","full_name":"Kubicek, Stefan"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Giulio","last_name":"Superti Furga","full_name":"Superti Furga, Giulio"},{"full_name":"Knapp, Sylvia","last_name":"Knapp","first_name":"Sylvia"}],"date_published":"2016-12-01T00:00:00Z","month":"12","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"6216","status":"public","intvolume":"        17","department":[{"_id":"MiSi"},{"_id":"PeJo"}],"oa":1,"date_updated":"2025-09-22T14:10:50Z","publisher":"Nature Publishing Group","page":"1361 - 1372","external_id":{"isi":["000388056400006"]},"abstract":[{"lang":"eng","text":"Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders."}],"oa_version":"Submitted Version","_id":"1142","scopus_import":"1","quality_controlled":"1","doi":"10.1038/ni.3590","citation":{"ieee":"R. Martins <i>et al.</i>, “Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions,” <i>Nature Immunology</i>, vol. 17, no. 12. Nature Publishing Group, pp. 1361–1372, 2016.","ama":"Martins R, Maier J, Gorki A, et al. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. 2016;17(12):1361-1372. doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>","chicago":"Martins, Rui, Julia Maier, Anna Gorki, Kilian Huber, Omar Sharif, Philipp Starkl, Simona Saluzzo, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>.","mla":"Martins, Rui, et al. “Heme Drives Hemolysis-Induced Susceptibility to Infection via Disruption of Phagocyte Functions.” <i>Nature Immunology</i>, vol. 17, no. 12, Nature Publishing Group, 2016, pp. 1361–72, doi:<a href=\"https://doi.org/10.1038/ni.3590\">10.1038/ni.3590</a>.","apa":"Martins, R., Maier, J., Gorki, A., Huber, K., Sharif, O., Starkl, P., … Knapp, S. (2016). Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3590\">https://doi.org/10.1038/ni.3590</a>","short":"R. Martins, J. Maier, A. Gorki, K. Huber, O. Sharif, P. Starkl, S. Saluzzo, F. Quattrone, R. Gawish, K. Lakovits, M. Aichinger, B. Radic Sarikas, C. Lardeau, A. Hladik, A. Korosec, M. Brown, K. Vaahtomeri, M. Duggan, D. Kerjaschki, H. Esterbauer, J. Colinge, S. Eisenbarth, T. Decker, K. Bennett, S. Kubicek, M.K. Sixt, G. Superti Furga, S. Knapp, Nature Immunology 17 (2016) 1361–1372.","ista":"Martins R, Maier J, Gorki A, Huber K, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger M, Radic Sarikas B, Lardeau C, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth S, Decker T, Bennett K, Kubicek S, Sixt MK, Superti Furga G, Knapp S. 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology. 17(12), 1361–1372."},"issue":"12","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}]},{"publist_id":"6215","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","status":"public","month":"03","date_published":"2016-03-24T00:00:00Z","author":[{"last_name":"Nam","first_name":"Phan","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rougerie","first_name":"Nicolas","full_name":"Rougerie, Nicolas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"department":[{"_id":"RoSe"}],"intvolume":"         9","arxiv":1,"oa":1,"date_updated":"2025-09-22T14:10:16Z","oa_version":"Preprint","_id":"1143","scopus_import":"1","publisher":"Mathematical Sciences Publishers","abstract":[{"text":"We study the ground state of a dilute Bose gas in a scaling limit where the Gross-Pitaevskii functional emerges. This is a repulsive nonlinear Schrödinger functional whose quartic term is proportional to the scattering length of the interparticle interaction potential. We propose a new derivation of this limit problem, with a method that bypasses some of the technical difficulties that previous derivations had to face. The new method is based on a combination of Dyson\\'s lemma, the quantum de Finetti theorem and a second moment estimate for ground states of the effective Dyson Hamiltonian. It applies equally well to the case where magnetic fields or rotation are present.","lang":"eng"}],"external_id":{"arxiv":["1503.07061"],"isi":["000378287000006"]},"page":"459 - 485","doi":"10.2140/apde.2016.9.459","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.07061"}],"issue":"2","citation":{"apa":"Nam, P., Rougerie, N., &#38; Seiringer, R. (2016). Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>","ista":"Nam P, Rougerie N, Seiringer R. 2016. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. Analysis and PDE. 9(2), 459–485.","short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","ieee":"P. Nam, N. Rougerie, and R. Seiringer, “Ground states of large bosonic systems: The gross Pitaevskii limit revisited,” <i>Analysis and PDE</i>, vol. 9, no. 2. Mathematical Sciences Publishers, pp. 459–485, 2016.","chicago":"Nam, Phan, Nicolas Rougerie, and Robert Seiringer. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>. Mathematical Sciences Publishers, 2016. <a href=\"https://doi.org/10.2140/apde.2016.9.459\">https://doi.org/10.2140/apde.2016.9.459</a>.","mla":"Nam, Phan, et al. “Ground States of Large Bosonic Systems: The Gross Pitaevskii Limit Revisited.” <i>Analysis and PDE</i>, vol. 9, no. 2, Mathematical Sciences Publishers, 2016, pp. 459–85, doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>.","ama":"Nam P, Rougerie N, Seiringer R. Ground states of large bosonic systems: The gross Pitaevskii limit revisited. <i>Analysis and PDE</i>. 2016;9(2):459-485. doi:<a href=\"https://doi.org/10.2140/apde.2016.9.459\">10.2140/apde.2016.9.459</a>"},"quality_controlled":"1","year":"2016","day":"24","volume":9,"date_created":"2018-12-11T11:50:23Z","language":[{"iso":"eng"}],"ec_funded":1,"isi":1,"publication_status":"published","publication":"Analysis and PDE","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"ddc":["530"],"date_created":"2018-12-11T11:44:37Z","file":[{"date_updated":"2019-05-15T14:12:31Z","access_level":"open_access","date_created":"2019-05-15T14:12:31Z","file_id":"6458","content_type":"application/pdf","success":1,"creator":"kschuh","file_name":"2016_PhysRevX_Aasen.pdf","relation":"main_file","file_size":2142676}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":6,"file_date_updated":"2019-05-15T14:12:31Z","article_number":"031016","day":"03","year":"2016","title":"Milestones toward Majorana-based quantum computing","acknowledgement":"We acknowledge support from Microsoft Research, the National Science Foundation through Grant No. DMR-1341822 (J. A.); the Alfred P. Sloan Foundation (J. A.); the Caltech Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation through Grant No. GBMF1250; the Walter Burke Institute for Theoretical Physics at Caltech; the NSERC PGSD program (D. A.); the Crafoord Foundation (M. L. and M. H.) and the Swedish Research Council (M. L.); The Danish National Research Foundation, and the Villum Foundation (C. M.); The Danish Council for Independent Research/Natural Sciences, and Danmarks Nationalbank (J. F.). Part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-1066293 (R. V. M.).","publication":"Physical Review X","publication_status":"published","extern":"1","date_updated":"2021-01-12T06:47:33Z","oa":1,"intvolume":"         6","author":[{"last_name":"Aasen","first_name":"David","full_name":"Aasen, David"},{"first_name":"Michael","last_name":"Hell","full_name":"Hell, Michael"},{"last_name":"Mishmash","first_name":"Ryan","full_name":"Mishmash, Ryan"},{"full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P"},{"full_name":"Danon, Jeroen","last_name":"Danon","first_name":"Jeroen"},{"full_name":"Leijnse, Martin","first_name":"Martin","last_name":"Leijnse"},{"full_name":"Jespersen, Thomas","first_name":"Thomas","last_name":"Jespersen"},{"last_name":"Folk","first_name":"Joshua","full_name":"Folk, Joshua"},{"full_name":"Marcs, Charles","last_name":"Marcs","first_name":"Charles"},{"full_name":"Flensberg, Karsten","last_name":"Flensberg","first_name":"Karsten"},{"first_name":"Jason","last_name":"Alicea","full_name":"Alicea, Jason"}],"month":"08","date_published":"2016-08-03T00:00:00Z","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publist_id":"7954","quality_controlled":"1","citation":{"ieee":"D. Aasen <i>et al.</i>, “Milestones toward Majorana-based quantum computing,” <i>Physical Review X</i>, vol. 6, no. 3. American Physical Society, 2016.","mla":"Aasen, David, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>, vol. 6, no. 3, 031016, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>.","chicago":"Aasen, David, Michael Hell, Ryan Mishmash, Andrew P Higginbotham, Jeroen Danon, Martin Leijnse, Thomas Jespersen, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>.","ama":"Aasen D, Hell M, Mishmash R, et al. Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. 2016;6(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>","apa":"Aasen, D., Hell, M., Mishmash, R., Higginbotham, A. P., Danon, J., Leijnse, M., … Alicea, J. (2016). Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>","ista":"Aasen D, Hell M, Mishmash R, Higginbotham AP, Danon J, Leijnse M, Jespersen T, Folk J, Marcs C, Flensberg K, Alicea J. 2016. Milestones toward Majorana-based quantum computing. Physical Review X. 6(3), 031016.","short":"D. Aasen, M. Hell, R. Mishmash, A.P. Higginbotham, J. Danon, M. Leijnse, T. Jespersen, J. Folk, C. Marcs, K. Flensberg, J. Alicea, Physical Review X 6 (2016)."},"issue":"3","doi":"10.1103/PhysRevX.6.031016","abstract":[{"lang":"eng","text":"We introduce a scheme for preparation, manipulation, and read out of Majorana zero modes in semiconducting wires with mesoscopic superconducting islands. Our approach synthesizes recent advances in materials growth with tools commonly used in quantum-dot experiments, including gate control of tunnel barriers and Coulomb effects, charge sensing, and charge pumping. We outline a sequence of milestones interpolating between zero-mode detection and quantum computing that includes (1) detection of fusion rules for non-Abelian anyons using either proximal charge sensors or pumped current, (2) validation of a prototype topological qubit, and (3) demonstration of non-Abelian statistics by braiding in a branched geometry. The first two milestones require only a single wire with two islands, and additionally enable sensitive measurements of the system\\'s excitation gap, quasiparticle poisoning rates, residual Majorana zero-mode splittings, and topological-qubit coherence times. These pre-braiding experiments can be adapted to other manipulation and read out schemes as well."}],"publisher":"American Physical Society","has_accepted_license":"1","_id":"100","oa_version":"Published Version"},{"day":"10","year":"2016","volume":531,"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:38Z","extern":"1","publication_status":"published","title":"Exponential protection of zero modes in Majorana islands","acknowledgement":"This research was supported by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation and the European Commission. C.M.M. acknowledges support from the Villum Foundation.","publication":"Nature","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7953","author":[{"first_name":"S M","last_name":"Albrecht","full_name":"Albrecht, S M"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham"},{"full_name":"Jespersen, Thomas","first_name":"Thomas","last_name":"Jespersen"},{"full_name":"Madsen, Morten","first_name":"Morten","last_name":"Madsen"},{"last_name":"Kuemmeth","first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand"},{"last_name":"Nygård","first_name":"Jesper","full_name":"Nygård, Jesper"},{"first_name":"Peter","last_name":"Krogstrup","full_name":"Krogstrup, Peter"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"}],"month":"03","date_published":"2016-03-10T00:00:00Z","date_updated":"2021-01-12T06:47:37Z","oa":1,"arxiv":1,"intvolume":"       531","oa_version":"Submitted Version","_id":"101","external_id":{"arxiv":["1603.03217"]},"page":"206 - 209","abstract":[{"lang":"eng","text":"Majorana zero modes are quasiparticle excitations in condensed matter systems that have been proposed as building blocks of fault-tolerant quantum computers. They are expected to exhibit non-Abelian particle statistics, in contrast to the usual statistics of fermions and bosons, enabling quantum operations to be performed by braiding isolated modes around one another. Quantum braiding operations are topologically protected insofar as these modes are pinned near zero energy, with the departure from zero expected to be exponentially small as the modes become spatially separated. Following theoretical proposals, several experiments have identified signatures of Majorana modes in nanowires with proximity-induced superconductivity and atomic chains, with small amounts of mode splitting potentially explained by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced superconducting Coulomb island (a â ∼ Majorana islandâ (tm)) that is isolated from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy Majorana modes. We observe exponential suppression of energy splitting with increasing wire length. For short devices of a few hundred nanometres, sub-gap state energies oscillate as the magnetic field is varied, as is expected for hybridized Majorana modes. Splitting decreases by a factor of about ten for each half a micrometre of increased wire length. For devices longer than about one micrometre, transport in strong magnetic fields occurs through a zero-energy state that is energetically isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance peaks, consistent with teleportation via Majorana modes. Our results help to explain the trivial-to-topological transition in finite systems and to quantify the scaling of topological protection with end-mode separation."}],"publisher":"Nature Publishing Group","citation":{"ama":"Albrecht SM, Higginbotham AP, Jespersen T, et al. Exponential protection of zero modes in Majorana islands. <i>Nature</i>. 2016;531(7593):206-209. doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>","mla":"Albrecht, S. M., et al. “Exponential Protection of Zero Modes in Majorana Islands.” <i>Nature</i>, vol. 531, no. 7593, Nature Publishing Group, 2016, pp. 206–09, doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>.","chicago":"Albrecht, S M, Andrew P Higginbotham, Thomas Jespersen, Morten Madsen, Ferdinand Kuemmeth, Jesper Nygård, Peter Krogstrup, and Charles Marcus. “Exponential Protection of Zero Modes in Majorana Islands.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature17162\">https://doi.org/10.1038/nature17162</a>.","ieee":"S. M. Albrecht <i>et al.</i>, “Exponential protection of zero modes in Majorana islands,” <i>Nature</i>, vol. 531, no. 7593. Nature Publishing Group, pp. 206–209, 2016.","short":"S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J. Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.","ista":"Albrecht SM, Higginbotham AP, Jespersen T, Madsen M, Kuemmeth F, Nygård J, Krogstrup P, Marcus C. 2016. Exponential protection of zero modes in Majorana islands. Nature. 531(7593), 206–209.","apa":"Albrecht, S. M., Higginbotham, A. P., Jespersen, T., Madsen, M., Kuemmeth, F., Nygård, J., … Marcus, C. (2016). Exponential protection of zero modes in Majorana islands. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature17162\">https://doi.org/10.1038/nature17162</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1603.03217","open_access":"1"}],"issue":"7593","doi":"10.1038/nature17162","quality_controlled":"1"},{"issue":"24","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07908"}],"citation":{"ama":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. Approaching a topological phase transition in Majorana nanowires. <i>Physical Review B</i>. 2016;93(24). doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">10.1103/PhysRevB.93.245404</a>","mla":"Mishmash, Ryan, et al. “Approaching a Topological Phase Transition in Majorana Nanowires.” <i>Physical Review B</i>, vol. 93, no. 24, 245404, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">10.1103/PhysRevB.93.245404</a>.","chicago":"Mishmash, Ryan, David Aasen, Andrew P Higginbotham, and Jason Alicea. “Approaching a Topological Phase Transition in Majorana Nanowires.” <i>Physical Review B</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">https://doi.org/10.1103/PhysRevB.93.245404</a>.","ieee":"R. Mishmash, D. Aasen, A. P. Higginbotham, and J. Alicea, “Approaching a topological phase transition in Majorana nanowires,” <i>Physical Review B</i>, vol. 93, no. 24. American Physical Society, 2016.","ista":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. 2016. Approaching a topological phase transition in Majorana nanowires. Physical Review B. 93(24), 245404.","short":"R. Mishmash, D. Aasen, A.P. Higginbotham, J. Alicea, Physical Review B 93 (2016).","apa":"Mishmash, R., Aasen, D., Higginbotham, A. P., &#38; Alicea, J. (2016). Approaching a topological phase transition in Majorana nanowires. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">https://doi.org/10.1103/PhysRevB.93.245404</a>"},"doi":"10.1103/PhysRevB.93.245404","quality_controlled":"1","oa_version":"Preprint","_id":"102","abstract":[{"lang":"eng","text":"Recent experiments have produced mounting evidence of Majorana zero modes in nanowire-superconductor hybrids. Signatures of an expected topological phase transition accompanying the onset of these modes nevertheless remain elusive. We investigate a fundamental question concerning this issue: Do well-formed Majorana modes necessarily entail a sharp phase transition in these setups? Assuming reasonable parameters, we argue that finite-size effects can dramatically smooth this putative transition into a crossover, even in systems large enough to support well-localized Majorana modes. We propose overcoming such finite-size effects by examining the behavior of low-lying excited states through tunneling spectroscopy. In particular, the excited-state energies exhibit characteristic field and density dependence, and scaling with system size, that expose an approaching topological phase transition. We suggest several experiments for extracting the predicted behavior. As a useful byproduct, the protocols also allow one to measure the wire's spin-orbit coupling directly in its superconducting environment."}],"external_id":{"arxiv":["1601.07908"]},"publisher":"American Physical Society","oa":1,"date_updated":"2021-01-12T06:47:42Z","intvolume":"        93","arxiv":1,"status":"public","publist_id":"7952","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2016-06-08T00:00:00Z","month":"06","author":[{"full_name":"Mishmash, Ryan","first_name":"Ryan","last_name":"Mishmash"},{"first_name":"David","last_name":"Aasen","full_name":"Aasen, David"},{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham"},{"first_name":"Jason","last_name":"Alicea","full_name":"Alicea, Jason"}],"publication_status":"published","title":"Approaching a topological phase transition in Majorana nanowires","publication":"Physical Review B","extern":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:38Z","year":"2016","day":"08","article_number":"245404","volume":93},{"external_id":{"arxiv":["1610.02320"],"pmid":["28799382"]},"abstract":[{"lang":"eng","text":"Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focusing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation."}],"publisher":"American Institute of Physics","scopus_import":"1","oa_version":"Preprint","_id":"10376","quality_controlled":"1","citation":{"short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016).","ista":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. The Journal of Chemical Physics. 145(21), 211926.","apa":"Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., &#38; Frenkel, D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>","ama":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. 2016;145(21). doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>","mla":"Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>.","chicago":"Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles, and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>.","ieee":"A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel, “Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation,” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21. American Institute of Physics, 2016."},"issue":"21","main_file_link":[{"url":"https://arxiv.org/abs/1610.02320","open_access":"1"}],"keyword":["physical and theoretical chemistry","general physics and astronomy"],"doi":"10.1063/1.4965040","pmid":1,"author":[{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"full_name":"Zaccone, Alessio","last_name":"Zaccone","first_name":"Alessio"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}],"month":"12","date_published":"2016-12-01T00:00:00Z","article_type":"original","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","oa":1,"date_updated":"2021-11-29T10:33:11Z","arxiv":1,"intvolume":"       145","extern":"1","article_processing_charge":"No","acknowledgement":"We acknowledge support from the Human Frontier Science Program and Emmanuel College (A.Š.), St John’s and Peterhouse Colleges (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council (T.C.T.M., T.P.J.K., and D.F.), and the Engineering and Physical Sciences Research Council (D.F.).","title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","publication":"The Journal of Chemical Physics","publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"volume":145,"day":"01","article_number":"211926","year":"2016","language":[{"iso":"eng"}],"date_created":"2021-11-29T10:01:57Z"},{"date_updated":"2021-11-29T11:08:15Z","oa":1,"arxiv":1,"intvolume":"         6","author":[{"last_name":"van der Wel","first_name":"Casper","full_name":"van der Wel, Casper"},{"last_name":"Vahid","first_name":"Afshin","full_name":"Vahid, Afshin"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"},{"first_name":"Doris","last_name":"Heinrich","full_name":"Heinrich, Doris"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"date_published":"2016-09-13T00:00:00Z","month":"09","article_type":"original","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","quality_controlled":"1","citation":{"ista":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. 2016. Lipid membrane-mediated attraction between curvature inducing objects. Scientific Reports. 6(1), 32825.","short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016).","apa":"van der Wel, C., Vahid, A., Šarić, A., Idema, T., Heinrich, D., &#38; Kraft, D. J. (2016). Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>","mla":"van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>, vol. 6, no. 1, 32825, Springer Nature, 2016, doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>.","chicago":"Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich, and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>.","ama":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. 2016;6(1). doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>","ieee":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft, “Lipid membrane-mediated attraction between curvature inducing objects,” <i>Scientific Reports</i>, vol. 6, no. 1. Springer Nature, 2016."},"issue":"1","main_file_link":[{"open_access":"1","url":"https://www.nature.com/articles/srep32825"}],"keyword":["multidisciplinary"],"doi":"10.1038/srep32825","pmid":1,"external_id":{"arxiv":["1603.04644"],"pmid":["27618764"]},"abstract":[{"lang":"eng","text":"The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy. Here, we present a combined experimental and numerical study in which we quantify these interactions directly for the first time. In our experimental model system we control the deformation of a lipid membrane by adhering colloidal particles. Using confocal microscopy, we establish that these membrane deformations cause an attractive interaction force leading to reversible binding. The attraction extends over 2.5 times the particle diameter and has a strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo simulations of the system are in excellent agreement with the experimental results and prove that the measured interaction is independent of length scale. Our combined experimental and numerical results reveal membrane curvature as a common physical origin for interactions between any membrane-deforming objects, from nanometre-sized proteins to micrometre-sized particles."}],"publisher":"Springer Nature","scopus_import":"1","has_accepted_license":"1","_id":"10377","oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2021-11-29T10:34:08Z","ddc":["540"],"file":[{"checksum":"d6cf16dd511e15726b001e7cc287cf1d","creator":"cchlebak","relation":"main_file","file_size":1598289,"file_name":"2016_SciRep_vanderWel.pdf","access_level":"open_access","date_created":"2021-11-29T10:50:00Z","date_updated":"2021-11-29T10:50:00Z","success":1,"content_type":"application/pdf","file_id":"10379"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":6,"publication_identifier":{"issn":["2045-2322"]},"file_date_updated":"2021-11-29T10:50:00Z","day":"13","article_number":"32825","year":"2016","article_processing_charge":"No","title":"Lipid membrane-mediated attraction between curvature inducing objects","acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program and VENI grant 680-47-431. We thank Jeroen Appel and Wim Pomp for advice on the protocol design and Marcel Winter and Ruben Verweij for experimental support.","publication":"Scientific Reports","publication_status":"published","extern":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/srep37382","relation":"erratum"}]}},{"publication_status":"published","acknowledgement":"We acknowledge support from the Human Frontier Science Program and Emmanuel College (A.Š.), the Leverhulme Trust and Magdalene College (A.K.B.), St John’s College (T.C.T.M.), the Biotechnology and Biological Sciences Research Council (T.P.J.K. and C.M.D.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council (T.P.J.K., T.C.T.M., S.L. and D.F.), and the Engineering and Physical Sciences Research Council (D.F.).","title":"Physical determinants of the self-replication of protein fibrils","article_processing_charge":"No","publication":"Nature Physics","extern":"1","language":[{"iso":"eng"}],"date_created":"2021-11-29T10:36:11Z","year":"2016","day":"18","volume":12,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"main_file_link":[{"open_access":"1","url":"https://discovery.ucl.ac.uk/id/eprint/1517406/"}],"issue":"9","citation":{"short":"A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J. Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.","ista":"Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils. Nature Physics. 12(9), 874–880.","apa":"Šarić, A., Buell, A. K., Meisl, G., Michaels, T. C. T., Dobson, C. M., Linse, S., … Frenkel, D. (2016). Physical determinants of the self-replication of protein fibrils. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nphys3828\">https://doi.org/10.1038/nphys3828</a>","ama":"Šarić A, Buell AK, Meisl G, et al. Physical determinants of the self-replication of protein fibrils. <i>Nature Physics</i>. 2016;12(9):874-880. doi:<a href=\"https://doi.org/10.1038/nphys3828\">10.1038/nphys3828</a>","chicago":"Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels, Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nphys3828\">https://doi.org/10.1038/nphys3828</a>.","mla":"Šarić, Anđela, et al. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>, vol. 12, no. 9, Springer Nature, 2016, pp. 874–80, doi:<a href=\"https://doi.org/10.1038/nphys3828\">10.1038/nphys3828</a>.","ieee":"A. Šarić <i>et al.</i>, “Physical determinants of the self-replication of protein fibrils,” <i>Nature Physics</i>, vol. 12, no. 9. Springer Nature, pp. 874–880, 2016."},"pmid":1,"doi":"10.1038/nphys3828","keyword":["general physics and astronomy"],"quality_controlled":"1","scopus_import":"1","_id":"10378","oa_version":"Preprint","abstract":[{"text":"The ability of biological molecules to replicate themselves is the foundation of life, requiring a complex cellular machinery. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional assistance. One example is the autocatalytic generation of pathological protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can take place only in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.","lang":"eng"}],"page":"874-880","external_id":{"pmid":["31031819"]},"publisher":"Springer Nature","oa":1,"date_updated":"2021-11-29T11:07:25Z","intvolume":"        12","status":"public","article_type":"original","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","date_published":"2016-07-18T00:00:00Z","month":"07","author":[{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Buell, Alexander K.","first_name":"Alexander K.","last_name":"Buell"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}]},{"extern":"1","publication_status":"published","acknowledgement":"The authors should like to dedicate this paper to the memory of Simon de Leeuw, who was a pioneer in the calculation of Coulomb effects in simulations. P.W. would like to thank the Austrian Academy of Sciences for financial support through a DOC Fellowship, and for covering the travel expenses for the CECAM workshop in Zaragoza in May 2015, where these results were first presented. P.W. would also like to thank Chao Zhang for pointing out the equivalence of the two expressions for the electric field discussed in Sec. VI D, Michiel Sprik for emphasising the importance of the quadrupole contribution in experimental studies of interfacial systems, as well as Aleks Reinhardt and other members of the Frenkel and Dellago groups for their advice. We further acknowledge support from the Federation of Austrian Industry (IV) Carinthia (P.W.), the University of Zagreb and Erasmus SMP (D. Fijan), the Human Frontier Science Program and Emmanuel College (A.Š.), the Austrian Science Fund FWF within the SFB Vicom project F41 (C.D.), and the Engineering and Physical Sciences Research Council Programme Grant No. EP/I001352/1 (D.F.). Additional data related to this publication are available at the University of Cambridge data repository (http://dx.doi.org/10.17863/CAM.118).","title":"Non-equilibrium simulations of thermally induced electric fields in water","article_processing_charge":"No","publication":"The Journal of Chemical Physics","year":"2016","article_number":"224102","day":"10","volume":144,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"language":[{"iso":"eng"}],"date_created":"2021-11-29T11:08:52Z","scopus_import":"1","oa_version":"Preprint","_id":"10380","abstract":[{"lang":"eng","text":"Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude."}],"external_id":{"arxiv":["1602.02734"],"pmid":["27305991"]},"publisher":"American Institute of Physics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02734"}],"issue":"22","citation":{"chicago":"Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D. Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>.","mla":"Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22, 224102, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>.","ama":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. 2016;144(22). doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>","ieee":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel, “Non-equilibrium simulations of thermally induced electric fields in water,” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22. American Institute of Physics, 2016.","ista":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium simulations of thermally induced electric fields in water. The Journal of Chemical Physics. 144(22), 224102.","short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","apa":"Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., &#38; Frenkel, D. (2016). Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>"},"pmid":1,"keyword":["physical and theoretical chemistry","general physics and astronomy"],"doi":"10.1063/1.4953036","quality_controlled":"1","status":"public","article_type":"original","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","date_published":"2016-06-10T00:00:00Z","month":"06","author":[{"full_name":"Wirnsberger, P.","last_name":"Wirnsberger","first_name":"P."},{"full_name":"Fijan, D.","first_name":"D.","last_name":"Fijan"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Neumann, M.","last_name":"Neumann","first_name":"M."},{"full_name":"Dellago, C.","last_name":"Dellago","first_name":"C."},{"full_name":"Frenkel, D.","first_name":"D.","last_name":"Frenkel"}],"date_updated":"2021-11-29T13:09:08Z","oa":1,"intvolume":"       144","arxiv":1},{"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","status":"public","date_published":"2016-08-19T00:00:00Z","month":"08","author":[{"last_name":"Bachmann","first_name":"Stephan Jan","full_name":"Bachmann, Stephan Jan"},{"last_name":"Kotar","first_name":"Jurij","full_name":"Kotar, Jurij"},{"first_name":"Lucia","last_name":"Parolini","full_name":"Parolini, Lucia"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Cicuta","first_name":"Pietro","full_name":"Cicuta, Pietro"},{"full_name":"Di Michele, Lorenzo","first_name":"Lorenzo","last_name":"Di Michele"},{"full_name":"Mognetti, Bortolo Matteo","last_name":"Mognetti","first_name":"Bortolo Matteo"}],"intvolume":"        12","arxiv":1,"oa":1,"date_updated":"2021-11-29T13:09:00Z","oa_version":"Preprint","_id":"10381","scopus_import":"1","publisher":"Royal Society of Chemistry","abstract":[{"lang":"eng","text":"We study phase behaviour of lipid-bilayer vesicles functionalised by ligand–receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand–receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand–receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion."}],"page":"7804-7817","external_id":{"pmid":["27722701"],"arxiv":["1608.05788"]},"pmid":1,"doi":"10.1039/c6sm01515h","keyword":["condensed matter physics","general chemistry"],"issue":"37","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05788"}],"citation":{"apa":"Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele, L., &#38; Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>","ista":"Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. 12(37), 7804–7817.","short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.","ieee":"S. J. Bachmann <i>et al.</i>, “Melting transition in lipid vesicles functionalised by mobile DNA linkers,” <i>Soft Matter</i>, vol. 12, no. 37. Royal Society of Chemistry, pp. 7804–7817, 2016.","chicago":"Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>.","mla":"Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>.","ama":"Bachmann SJ, Kotar J, Parolini L, et al. Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. 2016;12(37):7804-7817. doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>"},"quality_controlled":"1","year":"2016","day":"19","volume":12,"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"date_created":"2021-11-29T11:09:55Z","language":[{"iso":"eng"}],"extern":"1","publication_status":"published","publication":"Soft Matter","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","article_processing_charge":"No"},{"extern":"1","publication_status":"published","article_processing_charge":"No","title":"Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography","publication":"Nucleic Acids Research","day":"08","year":"2016","publication_identifier":{"eissn":["1362-4962"],"issn":["0305-1048"]},"volume":44,"OA_place":"publisher","OA_type":"gold","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"},"language":[{"iso":"eng"}],"ddc":["570"],"date_created":"2026-01-29T21:46:40Z","has_accepted_license":"1","_id":"21101","oa_version":"Published Version","page":"5936-5943","abstract":[{"text":"It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods—that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence ‘TATAAT’. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65–2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence.","lang":"eng"}],"publisher":"Oxford University Press","citation":{"ieee":"P. K. Mandal, G. W. Collie, S. C. Srivastava, B. Kauffmann, and I. Huc, “Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography,” <i>Nucleic Acids Research</i>, vol. 44, no. 12. Oxford University Press, pp. 5936–5943, 2016.","mla":"Mandal, Pradeep K., et al. “Structure Elucidation of the Pribnow Box Consensus Promoter Sequence by Racemic DNA Crystallography.” <i>Nucleic Acids Research</i>, vol. 44, no. 12, Oxford University Press, 2016, pp. 5936–43, doi:<a href=\"https://doi.org/10.1093/nar/gkw367\">10.1093/nar/gkw367</a>.","chicago":"Mandal, Pradeep K, Gavin W. Collie, Suresh C. Srivastava, Brice Kauffmann, and Ivan Huc. “Structure Elucidation of the Pribnow Box Consensus Promoter Sequence by Racemic DNA Crystallography.” <i>Nucleic Acids Research</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/nar/gkw367\">https://doi.org/10.1093/nar/gkw367</a>.","ama":"Mandal PK, Collie GW, Srivastava SC, Kauffmann B, Huc I. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. <i>Nucleic Acids Research</i>. 2016;44(12):5936-5943. doi:<a href=\"https://doi.org/10.1093/nar/gkw367\">10.1093/nar/gkw367</a>","apa":"Mandal, P. K., Collie, G. W., Srivastava, S. C., Kauffmann, B., &#38; Huc, I. (2016). Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkw367\">https://doi.org/10.1093/nar/gkw367</a>","short":"P.K. Mandal, G.W. Collie, S.C. Srivastava, B. Kauffmann, I. Huc, Nucleic Acids Research 44 (2016) 5936–5943.","ista":"Mandal PK, Collie GW, Srivastava SC, Kauffmann B, Huc I. 2016. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. Nucleic Acids Research. 44(12), 5936–5943."},"DOAJ_listed":"1","main_file_link":[{"url":"https://doi.org/10.1093/nar/gkw367","open_access":"1"}],"issue":"12","doi":"10.1093/nar/gkw367","quality_controlled":"1","article_type":"original","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Pradeep K","last_name":"Mandal","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X","full_name":"Mandal, Pradeep K"},{"last_name":"Collie","first_name":"Gavin W.","full_name":"Collie, Gavin W."},{"first_name":"Suresh C.","last_name":"Srivastava","full_name":"Srivastava, Suresh C."},{"full_name":"Kauffmann, Brice","last_name":"Kauffmann","first_name":"Brice"},{"first_name":"Ivan","last_name":"Huc","full_name":"Huc, Ivan"}],"date_published":"2016-07-08T00:00:00Z","month":"07","oa":1,"date_updated":"2026-02-23T09:16:14Z","intvolume":"        44"},{"date_updated":"2025-09-18T11:03:28Z","oa":1,"department":[{"_id":"ToBo"}],"intvolume":"       283","status":"public","pubrep_id":"488","type":"journal_article","publist_id":"5619","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Qi","first_name":"Qin","full_name":"Qi, Qin","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6148-2416"},{"full_name":"Toll Riera, Macarena","last_name":"Toll Riera","first_name":"Macarena"},{"full_name":"Heilbron, Karl","first_name":"Karl","last_name":"Heilbron"},{"last_name":"Preston","first_name":"Gail","full_name":"Preston, Gail"},{"last_name":"Maclean","first_name":"R Craig","full_name":"Maclean, R Craig"}],"month":"01","date_published":"2016-01-13T00:00:00Z","citation":{"mla":"Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1822, 20152452, Royal Society, The, 2016, doi:<a href=\"https://doi.org/10.1098/rspb.2015.2452\">10.1098/rspb.2015.2452</a>.","chicago":"Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2016. <a href=\"https://doi.org/10.1098/rspb.2015.2452\">https://doi.org/10.1098/rspb.2015.2452</a>.","ama":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2016;283(1822). doi:<a href=\"https://doi.org/10.1098/rspb.2015.2452\">10.1098/rspb.2015.2452</a>","ieee":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1822. Royal Society, The, 2016.","short":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","ista":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822), 20152452.","apa":"Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., &#38; Maclean, R. C. (2016). The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2015.2452\">https://doi.org/10.1098/rspb.2015.2452</a>"},"issue":"1822","doi":"10.1098/rspb.2015.2452","quality_controlled":"1","has_accepted_license":"1","scopus_import":"1","_id":"1552","oa_version":"Published Version","external_id":{"isi":["000368441200022"]},"abstract":[{"text":"Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.","lang":"eng"}],"publisher":"Royal Society, The","file":[{"date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","date_created":"2018-12-12T10:11:43Z","file_id":"4899","content_type":"application/pdf","checksum":"78ffe70c1c88af3856d31ca6b7195a27","creator":"system","file_name":"IST-2016-488-v1+1_20152452.full.pdf","file_size":626804,"relation":"main_file"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"ddc":["570"],"date_created":"2018-12-11T11:52:40Z","day":"13","article_number":"20152452","year":"2016","volume":283,"file_date_updated":"2020-07-14T12:45:02Z","publication_status":"published","article_processing_charge":"No","title":"The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa","acknowledgement":"We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z and Medical Research Council Hub grant no. G0900747 91070 for generation of the high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for their constructive feedback on previous versions of our manuscript.","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","isi":1},{"project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"name":"Stromal Cell-immune Cell Interactions in Health and Disease","call_identifier":"FP7","_id":"25A76F58-B435-11E9-9278-68D0E5697425","grant_number":"289720"},{"grant_number":"Y 564-B12","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa":1,"date_updated":"2025-09-18T11:01:30Z","department":[{"_id":"MiSi"}],"intvolume":"       351","status":"public","article_type":"original","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5570","author":[{"first_name":"Eva","last_name":"Kiermaier","orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","full_name":"Kiermaier, Eva"},{"first_name":"Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87","full_name":"Moussion, Christine"},{"last_name":"Veldkamp","first_name":"Christopher","full_name":"Veldkamp, Christopher"},{"full_name":"Gerardy  Schahn, Rita","last_name":"Gerardy  Schahn","first_name":"Rita"},{"last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Williams","first_name":"Larry","full_name":"Williams, Larry"},{"full_name":"Chaffee, Gary","first_name":"Gary","last_name":"Chaffee"},{"full_name":"Phillips, Andrew","first_name":"Andrew","last_name":"Phillips"},{"last_name":"Freiberger","first_name":"Friedrich","full_name":"Freiberger, Friedrich"},{"first_name":"Richard","last_name":"Imre","full_name":"Imre, Richard"},{"first_name":"Deni","last_name":"Taleski","full_name":"Taleski, Deni"},{"full_name":"Payne, Richard","last_name":"Payne","first_name":"Richard"},{"last_name":"Braun","first_name":"Asolina","full_name":"Braun, Asolina"},{"full_name":"Förster, Reinhold","last_name":"Förster","first_name":"Reinhold"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"full_name":"Mühlenhoff, Martina","first_name":"Martina","last_name":"Mühlenhoff"},{"last_name":"Volkman","first_name":"Brian","full_name":"Volkman, Brian"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"month":"01","date_published":"2016-01-08T00:00:00Z","citation":{"apa":"Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy  Schahn, R., de Vries, I., Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aad0512\">https://doi.org/10.1126/science.aad0512</a>","short":"E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy  Schahn, I. de Vries, L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne, A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science 351 (2016) 186–190.","ista":"Kiermaier E, Moussion C, Veldkamp C, Gerardy  Schahn R, de Vries I, Williams L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269), 186–190.","ieee":"E. Kiermaier <i>et al.</i>, “Polysialylation controls dendritic cell trafficking by regulating chemokine recognition,” <i>Science</i>, vol. 351, no. 6269. American Association for the Advancement of Science, pp. 186–190, 2016.","chicago":"Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy  Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aad0512\">https://doi.org/10.1126/science.aad0512</a>.","mla":"Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” <i>Science</i>, vol. 351, no. 6269, American Association for the Advancement of Science, 2016, pp. 186–90, doi:<a href=\"https://doi.org/10.1126/science.aad0512\">10.1126/science.aad0512</a>.","ama":"Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. <i>Science</i>. 2016;351(6269):186-190. doi:<a href=\"https://doi.org/10.1126/science.aad0512\">10.1126/science.aad0512</a>"},"issue":"6269","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/"}],"doi":"10.1126/science.aad0512","pmid":1,"quality_controlled":"1","scopus_import":"1","_id":"1599","oa_version":"Submitted Version","page":"186 - 190","external_id":{"isi":["000367806500045"],"pmid":["26657283"]},"abstract":[{"lang":"eng","text":"The addition of polysialic acid to N- and/or O-linked glycans, referred to as polysialylation, is a rare posttranslational modification that is mainly known to control the developmental plasticity of the nervous system. Here we show that CCR7, the central chemokine receptor controlling immune cell trafficking to secondary lymphatic organs, carries polysialic acid. This modification is essential for the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited conformation, which is released upon interaction with polysialic acid. Thus, we describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic basis.\r\n"}],"publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:52:57Z","day":"08","year":"2016","volume":351,"publication_status":"published","corr_author":"1","article_processing_charge":"No","acknowledgement":"We thank S. Schüchner and E. Ogris for kindly providing the antibody to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for critically reading the manuscript. ","title":"Polysialylation controls dendritic cell trafficking by regulating chemokine recognition","publication":"Science","isi":1,"ec_funded":1},{"volume":17,"day":"01","year":"2016","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:53:00Z","isi":1,"ec_funded":1,"article_processing_charge":"No","title":"Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel","publication":"Annales Henri Poincare","publication_status":"published","corr_author":"1","author":[{"full_name":"Sadel, Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8255-3968","last_name":"Sadel","first_name":"Christian"}],"month":"07","date_published":"2016-07-01T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publist_id":"5558","date_updated":"2025-09-18T11:00:43Z","oa":1,"arxiv":1,"intvolume":"        17","department":[{"_id":"LaEr"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"external_id":{"arxiv":["1501.04287"],"isi":["000377994000003"]},"page":"1631 - 1675","abstract":[{"lang":"eng","text":"We show that the Anderson model has a transition from localization to delocalization at exactly 2 dimensional growth rate on antitrees with normalized edge weights which are certain discrete graphs. The kinetic part has a one-dimensional structure allowing a description through transfer matrices which involve some Schur complement. For such operators we introduce the notion of having one propagating channel and extend theorems from the theory of one-dimensional Jacobi operators that relate the behavior of transfer matrices with the spectrum. These theorems are then applied to the considered model. In essence, in a certain energy region the kinetic part averages the random potentials along shells and the transfer matrices behave similar as for a one-dimensional operator with random potential of decaying variance. At d dimensional growth for d&gt;2 this effective decay is strong enough to obtain absolutely continuous spectrum, whereas for some uniform d dimensional growth with d&lt;2 one has pure point spectrum in this energy region. At exactly uniform 2 dimensional growth also some singular continuous spectrum appears, at least at small disorder. As a corollary we also obtain a change from singular spectrum (d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete adjacency operator (Laplacian) on ℤd and λ a random potential. "}],"publisher":"Birkhäuser","scopus_import":"1","oa_version":"Preprint","_id":"1608","quality_controlled":"1","citation":{"short":"C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.","ista":"Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 17(7), 1631–1675.","apa":"Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. <i>Annales Henri Poincare</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00023-015-0456-3\">https://doi.org/10.1007/s00023-015-0456-3</a>","mla":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” <i>Annales Henri Poincare</i>, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:<a href=\"https://doi.org/10.1007/s00023-015-0456-3\">10.1007/s00023-015-0456-3</a>.","chicago":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” <i>Annales Henri Poincare</i>. Birkhäuser, 2016. <a href=\"https://doi.org/10.1007/s00023-015-0456-3\">https://doi.org/10.1007/s00023-015-0456-3</a>.","ama":"Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. <i>Annales Henri Poincare</i>. 2016;17(7):1631-1675. doi:<a href=\"https://doi.org/10.1007/s00023-015-0456-3\">10.1007/s00023-015-0456-3</a>","ieee":"C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel,” <i>Annales Henri Poincare</i>, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016."},"issue":"7","main_file_link":[{"url":"http://arxiv.org/abs/1501.04287","open_access":"1"}],"doi":"10.1007/s00023-015-0456-3"},{"isi":1,"publication":"Algebra Universalis","article_processing_charge":"No","title":"CSP for binary conservative relational structures","corr_author":"1","publication_status":"published","volume":75,"day":"01","year":"2016","date_created":"2018-12-11T11:53:01Z","language":[{"iso":"eng"}],"publisher":"Springer","external_id":{"arxiv":["1112.1099"],"isi":["000375422500006"]},"page":"75 - 84","abstract":[{"lang":"eng","text":"We prove that whenever A is a 3-conservative relational structure with only binary and unary relations,then the algebra of polymorphisms of A either has no Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety (i.e.,CSP(A)has bounded width)."}],"oa_version":"Preprint","_id":"1612","scopus_import":"1","quality_controlled":"1","doi":"10.1007/s00012-015-0358-8","citation":{"mla":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” <i>Algebra Universalis</i>, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:<a href=\"https://doi.org/10.1007/s00012-015-0358-8\">10.1007/s00012-015-0358-8</a>.","chicago":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” <i>Algebra Universalis</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00012-015-0358-8\">https://doi.org/10.1007/s00012-015-0358-8</a>.","ama":"Kazda A. CSP for binary conservative relational structures. <i>Algebra Universalis</i>. 2016;75(1):75-84. doi:<a href=\"https://doi.org/10.1007/s00012-015-0358-8\">10.1007/s00012-015-0358-8</a>","ieee":"A. Kazda, “CSP for binary conservative relational structures,” <i>Algebra Universalis</i>, vol. 75, no. 1. Springer, pp. 75–84, 2016.","short":"A. Kazda, Algebra Universalis 75 (2016) 75–84.","ista":"Kazda A. 2016. CSP for binary conservative relational structures. Algebra Universalis. 75(1), 75–84.","apa":"Kazda, A. (2016). CSP for binary conservative relational structures. <i>Algebra Universalis</i>. Springer. <a href=\"https://doi.org/10.1007/s00012-015-0358-8\">https://doi.org/10.1007/s00012-015-0358-8</a>"},"main_file_link":[{"url":"http://arxiv.org/abs/1112.1099","open_access":"1"}],"issue":"1","author":[{"full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","last_name":"Kazda","first_name":"Alexandr"}],"month":"02","date_published":"2016-02-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","publist_id":"5554","status":"public","arxiv":1,"intvolume":"        75","department":[{"_id":"VlKo"}],"date_updated":"2025-09-18T11:00:04Z","oa":1},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file":[{"file_name":"IST-2018-979-v1+1_Mungenast_2015_acceptedManuscript.pdf","relation":"main_file","file_size":632915,"checksum":"620254114e04d5d6e7f37d15e4b8ace4","creator":"system","file_id":"4970","content_type":"application/pdf","date_updated":"2020-07-14T12:45:07Z","access_level":"open_access","date_created":"2018-12-12T10:12:50Z"}],"date_created":"2018-12-11T11:53:02Z","ddc":["616"],"language":[{"iso":"eng"}],"day":"01","year":"2016","volume":73,"file_date_updated":"2020-07-14T12:45:07Z","corr_author":"1","publication_status":"published","publication":"Molecular and Cellular Neuroscience","article_processing_charge":"No","acknowledgement":"This work was supported by NIH grant R01-AG047661 to LHT. The art in Fig. 1 was created by Julian Wong.","title":"Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells","isi":1,"extern":"1","intvolume":"        73","date_updated":"2025-09-18T10:59:24Z","oa":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5553","pubrep_id":"979","status":"public","author":[{"full_name":"Mungenast, Alison","first_name":"Alison","last_name":"Mungenast"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert"},{"last_name":"Tsai","first_name":"Li","full_name":"Tsai, Li"}],"month":"06","date_published":"2016-06-01T00:00:00Z","doi":"doi:10.1016/j.mcn.2015.11.010","citation":{"ieee":"A. Mungenast, S. Siegert, and L. Tsai, “Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells,” <i>Molecular and Cellular Neuroscience</i>, vol. 73. Academic Press, pp. 13–31, 2016.","ama":"Mungenast A, Siegert S, Tsai L. Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells. <i>Molecular and Cellular Neuroscience</i>. 2016;73:13-31. doi:<a href=\"https://doi.org/doi:10.1016/j.mcn.2015.11.010\">doi:10.1016/j.mcn.2015.11.010</a>","chicago":"Mungenast, Alison, Sandra Siegert, and Li Tsai. “Modeling Alzheimer’s Disease with Human Induced Pluripotent Stem (IPS) Cells.” <i>Molecular and Cellular Neuroscience</i>. Academic Press, 2016. <a href=\"https://doi.org/doi:10.1016/j.mcn.2015.11.010\">https://doi.org/doi:10.1016/j.mcn.2015.11.010</a>.","mla":"Mungenast, Alison, et al. “Modeling Alzheimer’s Disease with Human Induced Pluripotent Stem (IPS) Cells.” <i>Molecular and Cellular Neuroscience</i>, vol. 73, Academic Press, 2016, pp. 13–31, doi:<a href=\"https://doi.org/doi:10.1016/j.mcn.2015.11.010\">doi:10.1016/j.mcn.2015.11.010</a>.","apa":"Mungenast, A., Siegert, S., &#38; Tsai, L. (2016). Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells. <i>Molecular and Cellular Neuroscience</i>. Academic Press. <a href=\"https://doi.org/doi:10.1016/j.mcn.2015.11.010\">https://doi.org/doi:10.1016/j.mcn.2015.11.010</a>","short":"A. Mungenast, S. Siegert, L. Tsai, Molecular and Cellular Neuroscience 73 (2016) 13–31.","ista":"Mungenast A, Siegert S, Tsai L. 2016. Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells. Molecular and Cellular Neuroscience. 73, 13–31."},"quality_controlled":"1","oa_version":"Submitted Version","_id":"1613","has_accepted_license":"1","publisher":"Academic Press","page":"13 - 31","external_id":{"isi":["000376225300003"]},"abstract":[{"lang":"eng","text":"In the last decade, induced pluripotent stem (iPS) cells have revolutionized the utility of human in vitro models of neurological disease. The iPS-derived and differentiated cells allow researchers to study the impact of a distinct cell type in health and disease as well as performing therapeutic drug screens on a human genetic background. In particular, clinical trials for Alzheimer's disease (AD) have been often failing. Two of the potential reasons are first, the species gap involved in proceeding from initial discoveries in rodent models to human studies, and second, an unsatisfying patient stratification, meaning subgrouping patients based on the disease severity due to the lack of phenotypic and genetic markers. iPS cells overcome this obstacles and will improve our understanding of disease subtypes in AD. They allow researchers conducting in depth characterization of neural cells from both familial and sporadic AD patients as well as preclinical screens on human cells.\r\n\r\nIn this review, we briefly outline the status quo of iPS cell research in neurological diseases along with the general advantages and pitfalls of these models. We summarize how genome-editing techniques such as CRISPR/Cas will allow researchers to reduce the problem of genomic variability inherent to human studies, followed by recent iPS cell studies relevant to AD. We then focus on current techniques for the differentiation of iPS cells into neural cell types that are relevant to AD research. Finally, we discuss how the generation of three-dimensional cell culture systems will be important for understanding AD phenotypes in a complex cellular milieu, and how both two- and three-dimensional iPS cell models can provide platforms for drug discovery and translational studies into the treatment of AD."}]},{"publisher":"Wiley","abstract":[{"text":"The hippocampus plays a key role in learning and memory. Previous studies suggested that the main types of principal neurons, dentate gyrus granule cells (GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal neurons. It has been assumed but never shown that such different activity may be caused by differential synaptic excitation. To test this hypothesis, we performed high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo. In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine the underlying mechanisms, we quantitatively assessed the frequency of spontaneous excitatory synaptic input, the passive membrane properties, and the active membrane characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3 and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition. Thus, differential synaptic excitation is not responsible for differences in firing. Moreover, the three types of hippocampal neurons markedly differed in their passive properties. While GCs showed the most negative membrane potential, CA3 pyramidal neurons had the highest input resistance and the slowest membrane time constant. The three types of neurons also differed in the active membrane characteristics. GCs showed the highest action potential threshold, but displayed the largest gain of the input-output curves. In conclusion, our results reveal that differential firing of the three main types of hippocampal principal neurons in vivo is not primarily caused by differences in the characteristics of the synaptic input, but by the distinct properties of synaptic integration and input-output transformation.","lang":"eng"}],"external_id":{"isi":["000374666700011"]},"page":"668 - 682","_id":"1616","oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","quality_controlled":"1","doi":"10.1002/hipo.22550","issue":"5","citation":{"apa":"Kowalski, J., Gan, J., Jonas, P. M., &#38; Pernia-Andrade, A. (2016). Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.22550\">https://doi.org/10.1002/hipo.22550</a>","ista":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 26(5), 668–682.","short":"J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016) 668–682.","ieee":"J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats,” <i>Hippocampus</i>, vol. 26, no. 5. Wiley, pp. 668–682, 2016.","mla":"Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” <i>Hippocampus</i>, vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:<a href=\"https://doi.org/10.1002/hipo.22550\">10.1002/hipo.22550</a>.","chicago":"Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” <i>Hippocampus</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/hipo.22550\">https://doi.org/10.1002/hipo.22550</a>.","ama":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. <i>Hippocampus</i>. 2016;26(5):668-682. doi:<a href=\"https://doi.org/10.1002/hipo.22550\">10.1002/hipo.22550</a>"},"date_published":"2016-05-01T00:00:00Z","month":"05","author":[{"full_name":"Kowalski, Janina","id":"3F3CA136-F248-11E8-B48F-1D18A9856A87","last_name":"Kowalski","first_name":"Janina"},{"first_name":"Jian","last_name":"Gan","id":"3614E438-F248-11E8-B48F-1D18A9856A87","full_name":"Gan, Jian"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"last_name":"Pernia-Andrade","first_name":"Alejandro","full_name":"Pernia-Andrade, Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5550","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","pubrep_id":"469","intvolume":"        26","department":[{"_id":"PeJo"}],"date_updated":"2025-09-18T10:58:31Z","oa":1,"isi":1,"publication":"Hippocampus","title":"Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats","acknowledgement":"The authors thank Jose Guzman for critically reading prior versions of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices, A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger for manuscript editing.","article_processing_charge":"No","corr_author":"1","publication_status":"published","file_date_updated":"2020-07-14T12:45:07Z","volume":26,"publication_identifier":{"issn":["1050-9631"],"eissn":["1098-1063"]},"year":"2016","day":"01","date_created":"2018-12-11T11:53:03Z","ddc":["570"],"language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file":[{"date_created":"2018-12-12T10:13:47Z","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","content_type":"application/pdf","file_id":"5033","creator":"system","checksum":"284b72b12fbe15474833ed3d4549f86b","file_size":905348,"relation":"main_file","file_name":"IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf"}]}]